From a4f9b7338a9ac517930c6ee079b0ef27b24e9702 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bastien=20Herv=C3=A9?= <bastienherve61@gmail.com>
Date: Wed, 19 Apr 2023 10:56:49 +0200
Subject: [PATCH 01/34] Update utilities.R

Addition of ExportGroupBW, CreateBWGroup and '%bcin%', to export bigwig file from split fragments file
---
 R/utilities.R | 173 +++++++++++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 172 insertions(+), 1 deletion(-)

diff --git a/R/utilities.R b/R/utilities.R
index 01671c09..300ce842 100644
--- a/R/utilities.R
+++ b/R/utilities.R
@@ -2236,4 +2236,175 @@ SparseSpearmanCor <- function(X, Y = NULL, cov = FALSE) {
     }
   rankY <- SparsifiedRanks(X = Y)
   return(qlcMatrix::corSparse(X = rankX, Y = rankY, cov = cov))
-}
\ No newline at end of file
+}
+
+# Export bigwig file for each group of bed file present in outdir
+# @param object The seurat object
+# @param assay The assay of the fragment file
+# @param group.by The metadata used to split the fragment file
+# @param idents The idents from the group.by to be exported
+# @param normMethod Normalization method for the biwig files
+# It can be the name of any quantitative column in the @meta.data
+# or ncells as the number of cells
+# @param tileSize The size of the tiles in the bigwig file
+# @param minCells The minimum of cells in a group to be exported
+# @param cutoff The maximum number of fragment in a given tile
+# @param chromosome The chromosomes to be exported 
+# @param threads Number of threads
+# @param outdir The output directory for bigwig file
+# Also used as output directory for SlitFragment function
+# @param verbose Display messages
+#' @importFrom GenomicRanges seqlengths GRanges slidingWindows
+#' @importFrom future plan
+#' @importFrom future.apply future_lapply
+
+ExportGroupBW  <- function(
+  object = NULL,
+  assay = "peaks",
+  group.by = "seurat_clusters",
+  idents = c(0,2),
+  normMethod = "TSS.enrichment",
+  tileSize = 100,
+  minCells = 5,
+  cutoff = 4,
+  chromosome = "primary",
+  threads = NULL,
+  outdir = NULL,
+  verbose=TRUE
+  ){
+  
+    DefaultAssay(object) <- assay
+  
+    GroupsNames <- names(table(object@meta.data[,group.by])[table(object@meta.data[,group.by]) > minCells])
+    GroupsNames <- GroupsNames[GroupsNames %in% idents]
+       
+    #Column to normalized by
+    if (normMethod == 'ncells'){
+      normBy <- normMethod
+    } else{
+      normBy <- object@meta.data[, normMethod, drop=FALSE]
+    }
+    
+    #Get chromosome information
+    if(chromosome=="primary"){
+      prim_chr <- names(seqlengths(object)[!grepl("_alt|_fix|_random|chrUn", names(seqlengths(object)))])
+      seqlevels(object) <- prim_chr
+    }
+    availableChr <- names(seqlengths(object))
+    chromLengths <- seqlengths(object)
+    chromSizes <- GRanges(seqnames = availableChr, IRanges(start = rep(1, length(availableChr)), end = as.numeric(chromLengths)))
+
+    if (verbose) {
+      message("Creation of tiles")
+    }
+    
+    #Create tiles for each chromosome, from GenomicRanges
+    tiles <- unlist(slidingWindows(chromSizes, width = tileSize, step = tileSize))
+    
+    if (verbose) {
+      message("Bigwig files generation at ", outdir)
+    }
+    
+    #Set number of thread in future
+    plan("multicore", workers = threads)
+    
+    #Run the creation of bigwig for each cellgroups
+    covFiles <- future_lapply(GroupsNames, CreateBWGroup, availableChr, chromLengths, tiles, normBy, tileSize, normMethod, cutoff, outdir)
+
+    covFiles
+
+  }
+
+# Helper function for ExportGroupBW
+# @param groupNamei The group to be exported
+# @param availableChr Chromosomes to be processed
+# @param chromLengths Chromosomes lengths
+# @param tiles The tiles object
+# @param normBy A vector of values to normalized the cells by
+# or ncells as number of cells normalization
+# @param tileSize The size of the tiles in the bigwig file
+# @param normMethod Normalization method for the biwig files
+# It can be the name of any quantitative column in the @meta.data
+# or ncells as the number of cells
+# @param cutoff The maximum number of fragment in a given tile
+# @param outdir The output directory for bigwig file
+# Also used as output directory for SlitFragment function
+#' @importFrom rtracklayer import export.bw
+#' @importFrom GenomicRanges seqnames seqlengths GRanges coverage
+#' @importFrom BiocGenerics which
+#' @importFrom S4Vectors match
+#' @importFrom Matrix sparseMatrix rowSums
+CreateBWGroup <- function(groupNamei, availableChr, chromLengths, tiles, normBy, tileSize, normMethod, cutoff, outdir){
+
+  #Read the fragments file associated to the group
+  fragi <- rtracklayer::import(paste0(outdir, "/", groupNamei, ".bed"),format = "bed")
+
+  cellGroupi <- unique(fragi$name)
+
+  #Open the writting bigwig file
+  covFile <- file.path(outdir, paste0(groupNamei, "-TileSize-",tileSize,"-normMethod-",normMethod,".bw"))
+
+  covList <- lapply(seq_along(availableChr), function(k){
+
+    fragik <- fragi[seqnames(fragi) == availableChr[k],]
+    tilesk <- tiles[BiocGenerics::which(seqnames(tiles) %bcin% availableChr[k])]
+
+    if(length(fragik) == 0){
+      tilesk$reads <- 0
+    #If fragments
+    }else{
+
+      #N Tiles
+      nTiles <- chromLengths[availableChr[k]] / tileSize
+      #Add one tile if there is extra bases
+      if (nTiles%%1 != 0) {
+        nTiles <- trunc(nTiles) + 1
+      }
+
+      #Create Sparse Matrix
+      matchID <- S4Vectors::match(mcols(fragik)$name, cellGroupi)
+
+      #For each tiles of this chromosome, create start tile and end tile row, set the associated counts matching with the fragments
+      mat <- Matrix::sparseMatrix(
+        i = c(trunc(start(fragik) / tileSize), trunc(end(fragik) / tileSize)) + 1,
+        j = as.vector(c(matchID, matchID)),
+        x = rep(1,  2*length(fragik)),
+        dims = c(nTiles, length(cellGroupi)))
+
+      #Max count for a cells in a tile is set to cutoff (4)
+      if(!is.null(cutoff)){
+        mat@x[mat@x > cutoff] <- cutoff
+      }
+
+      #Sums the cells
+      mat <- Matrix::rowSums(mat)
+
+      tilesk$reads <- mat
+
+      #Normalization of counts by the sum of readsintss for each cells in group
+      if(normMethod == "ncells"){
+        tilesk$reads <- tilesk$reads / length(cellGroupi)
+      }else if(tolower(normMethod) %in% c("none")){
+      }else{
+        tilesk$reads <- tilesk$reads * 10^4 / sum(normBy[cellGroupi, 1])
+      }
+    }
+
+    tilesk <- coverage(tilesk, weight = tilesk$reads)[[availableChr[k]]]
+
+    tilesk
+
+  })
+
+  names(covList) <- availableChr
+
+  covList <- as(covList, "RleList")
+
+  rtracklayer::export.bw(object = covList, con = covFile)
+
+  covFile
+}
+
+# Helper function for CreateBWGroup
+#' @importFrom S4Vectors match
+'%bcin%' <- function(x, table) S4Vectors::match(x, table, nomatch = 0) > 0

From 033b7224a9e0a1c17a95cb136e0e7b8ef5633e45 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bastien=20Herv=C3=A9?= <bastienherve61@gmail.com>
Date: Thu, 20 Apr 2023 11:55:27 +0200
Subject: [PATCH 02/34] Update utilities.R

Some changes from @timoast comments on the PR
---
 R/utilities.R | 54 ++++++++++++++++++++++++++++-----------------------
 1 file changed, 30 insertions(+), 24 deletions(-)

diff --git a/R/utilities.R b/R/utilities.R
index 300ce842..c553afc4 100644
--- a/R/utilities.R
+++ b/R/utilities.R
@@ -2249,7 +2249,8 @@ SparseSpearmanCor <- function(X, Y = NULL, cov = FALSE) {
 # @param tileSize The size of the tiles in the bigwig file
 # @param minCells The minimum of cells in a group to be exported
 # @param cutoff The maximum number of fragment in a given tile
-# @param chromosome The chromosomes to be exported 
+# @param chromosome A chromosomes vector to be exported, standard
+# chromosomes can be fetched via standardChromosomes()
 # @param threads Number of threads
 # @param outdir The output directory for bigwig file
 # Also used as output directory for SlitFragment function
@@ -2260,36 +2261,48 @@ SparseSpearmanCor <- function(X, Y = NULL, cov = FALSE) {
 
 ExportGroupBW  <- function(
   object = NULL,
-  assay = "peaks",
-  group.by = "seurat_clusters",
-  idents = c(0,2),
-  normMethod = "TSS.enrichment",
+  assay = NULL,
+  group.by = NULL,
+  idents = NULL,
+  normMethod = "nCount_peaks",
   tileSize = 100,
   minCells = 5,
-  cutoff = 4,
-  chromosome = "primary",
+  cutoff = NULL,
+  chromosome = NULL,
   threads = NULL,
   outdir = NULL,
   verbose=TRUE
   ){
   
+    if (!requireNamespace("rtracklayer", quietly = TRUE)) { 
+      message("Please install rtracklayer. http://www.bioconductor.org/packages/rtracklayer/") 
+      return(NULL) 
+    } 
+  
+    assay <- assay %||% DefaultAssay(object = object)
     DefaultAssay(object) <- assay
   
-    GroupsNames <- names(table(object@meta.data[,group.by])[table(object@meta.data[,group.by]) > minCells])
+    group.by <- group.by %||% 'ident'
+    Idents(object = object) <- group.by
+  
+    idents <- idents %||% levels(object = object)
+    levels(object = object) <- idents
+  
+    GroupsNames <- names(table(object[[group.by]])[table(object[[group.by]]) > minCells])
     GroupsNames <- GroupsNames[GroupsNames %in% idents]
        
     #Column to normalized by
     if (normMethod == 'ncells'){
       normBy <- normMethod
     } else{
-      normBy <- object@meta.data[, normMethod, drop=FALSE]
+      normBy <- object[[normMethod, drop=FALSE]]
     }
     
     #Get chromosome information
-    if(chromosome=="primary"){
-      prim_chr <- names(seqlengths(object)[!grepl("_alt|_fix|_random|chrUn", names(seqlengths(object)))])
-      seqlevels(object) <- prim_chr
+    if(!is.null(chromosome)){
+      seqlevels(object) <- chromosome
     }
+
     availableChr <- names(seqlengths(object))
     chromLengths <- seqlengths(object)
     chromSizes <- GRanges(seqnames = availableChr, IRanges(start = rep(1, length(availableChr)), end = as.numeric(chromLengths)))
@@ -2304,10 +2317,7 @@ ExportGroupBW  <- function(
     if (verbose) {
       message("Bigwig files generation at ", outdir)
     }
-    
-    #Set number of thread in future
-    plan("multicore", workers = threads)
-    
+        
     #Run the creation of bigwig for each cellgroups
     covFiles <- future_lapply(GroupsNames, CreateBWGroup, availableChr, chromLengths, tiles, normBy, tileSize, normMethod, cutoff, outdir)
 
@@ -2337,7 +2347,7 @@ ExportGroupBW  <- function(
 CreateBWGroup <- function(groupNamei, availableChr, chromLengths, tiles, normBy, tileSize, normMethod, cutoff, outdir){
 
   #Read the fragments file associated to the group
-  fragi <- rtracklayer::import(paste0(outdir, "/", groupNamei, ".bed"),format = "bed")
+  fragi <- rtracklayer::import(paste0(outdir, .Platform$file.sep, groupNamei, ".bed"),format = "bed")
 
   cellGroupi <- unique(fragi$name)
 
@@ -2347,8 +2357,8 @@ CreateBWGroup <- function(groupNamei, availableChr, chromLengths, tiles, normBy,
   covList <- lapply(seq_along(availableChr), function(k){
 
     fragik <- fragi[seqnames(fragi) == availableChr[k],]
-    tilesk <- tiles[BiocGenerics::which(seqnames(tiles) %bcin% availableChr[k])]
-
+    tilesk <- tiles[BiocGenerics::which(S4Vectors::match(seqnames(tiles), availableChr[k], nomatch = 0) > 0)]
+    
     if(length(fragik) == 0){
       tilesk$reads <- 0
     #If fragments
@@ -2402,9 +2412,5 @@ CreateBWGroup <- function(groupNamei, availableChr, chromLengths, tiles, normBy,
 
   rtracklayer::export.bw(object = covList, con = covFile)
 
-  covFile
+  return(covFile)
 }
-
-# Helper function for CreateBWGroup
-#' @importFrom S4Vectors match
-'%bcin%' <- function(x, table) S4Vectors::match(x, table, nomatch = 0) > 0

From 081c8e1df3d4db37d8dbe3e3b77e5d2a75541e2a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bastien=20Herv=C3=A9?= <bastienherve61@gmail.com>
Date: Wed, 3 May 2023 10:54:44 +0200
Subject: [PATCH 03/34] Update utilities.R

SplitFragments inside the export function and check existing files
---
 R/utilities.R | 57 ++++++++++++++++++++++++++++++++++++++++-----------
 1 file changed, 45 insertions(+), 12 deletions(-)

diff --git a/R/utilities.R b/R/utilities.R
index c553afc4..a3eac542 100644
--- a/R/utilities.R
+++ b/R/utilities.R
@@ -2280,7 +2280,7 @@ ExportGroupBW  <- function(
     } 
   
     assay <- assay %||% DefaultAssay(object = object)
-    DefaultAssay(object) <- assay
+    DefaultAssay(object = object) <- assay
   
     group.by <- group.by %||% 'ident'
     Idents(object = object) <- group.by
@@ -2290,12 +2290,34 @@ ExportGroupBW  <- function(
   
     GroupsNames <- names(table(object[[group.by]])[table(object[[group.by]]) > minCells])
     GroupsNames <- GroupsNames[GroupsNames %in% idents]
+  
+    #Check if output files already exist
+    lapply(GroupsNames, function(x){
+      if (file.exists(paste0(outdir, .Platform$file.sep, x, ".bed"))){
+        message(sprintf("The group \"%s\" is already present in the destination folder and will be overwritten !",x))
+      }
+    })      
+      
+    #Splitting fragments file for each idents in group.by
+    SplitFragments(
+      object = object,
+      assay = assay,
+      group.by = group.by,
+      idents = idents,
+      outdir = outdir,
+      file.suffix = "",
+      append = TRUE,
+      buffer_length = 256L,
+      verbose = verbose
+    )
        
     #Column to normalized by
-    if (normMethod == 'ncells'){
-      normBy <- normMethod
-    } else{
-      normBy <- object[[normMethod, drop=FALSE]]
+    if(!is.null(normMethod)){
+      if (normMethod == 'ncells'){
+        normBy <- normMethod
+      } else{
+        normBy <- object[[normMethod, drop=FALSE]]
+      }
     }
     
     #Get chromosome information
@@ -2319,7 +2341,14 @@ ExportGroupBW  <- function(
     }
         
     #Run the creation of bigwig for each cellgroups
-    covFiles <- future_lapply(GroupsNames, CreateBWGroup, availableChr, chromLengths, tiles, normBy, tileSize, normMethod, cutoff, outdir)
+  
+    if (nbrOfWorkers() > 1) { 
+      mylapply <- future_lapply 
+    } else { 
+      mylapply <- ifelse(test = verbose, yes = pblapply, no = lapply) 
+    } 
+  
+    covFiles <- mylapply(GroupsNames, CreateBWGroup, availableChr, chromLengths, tiles, normBy, tileSize, normMethod, cutoff, outdir)
 
     covFiles
 
@@ -2381,7 +2410,7 @@ CreateBWGroup <- function(groupNamei, availableChr, chromLengths, tiles, normBy,
         x = rep(1,  2*length(fragik)),
         dims = c(nTiles, length(cellGroupi)))
 
-      #Max count for a cells in a tile is set to cutoff (4)
+      #Max count for a cells in a tile is set to cutoff
       if(!is.null(cutoff)){
         mat@x[mat@x > cutoff] <- cutoff
       }
@@ -2392,11 +2421,15 @@ CreateBWGroup <- function(groupNamei, availableChr, chromLengths, tiles, normBy,
       tilesk$reads <- mat
 
       #Normalization of counts by the sum of readsintss for each cells in group
-      if(normMethod == "ncells"){
-        tilesk$reads <- tilesk$reads / length(cellGroupi)
-      }else if(tolower(normMethod) %in% c("none")){
-      }else{
-        tilesk$reads <- tilesk$reads * 10^4 / sum(normBy[cellGroupi, 1])
+      if(!is.null(normMethod)){
+        if(normMethod == "ncells"){
+          tilesk$reads <- tilesk$reads / length(cellGroupi)
+        }else if(tolower(normMethod) %in% c("none")){
+        }else{
+          if(!is.null(normBy)){
+            tilesk$reads <- tilesk$reads * 10^4 / sum(normBy[cellGroupi, 1])
+          }
+        }
       }
     }
 

From 27d4565994570e6981cda3bca004383415578955 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bastien=20Herv=C3=A9?= <bastienherve61@gmail.com>
Date: Wed, 3 May 2023 11:55:07 +0200
Subject: [PATCH 04/34] Update utilities.R

Add relative count normalization per group per 10k
---
 R/utilities.R | 22 ++++++++++++----------
 1 file changed, 12 insertions(+), 10 deletions(-)

diff --git a/R/utilities.R b/R/utilities.R
index a3eac542..dacd9227 100644
--- a/R/utilities.R
+++ b/R/utilities.R
@@ -2244,8 +2244,8 @@ SparseSpearmanCor <- function(X, Y = NULL, cov = FALSE) {
 # @param group.by The metadata used to split the fragment file
 # @param idents The idents from the group.by to be exported
 # @param normMethod Normalization method for the biwig files
-# It can be the name of any quantitative column in the @meta.data
-# or ncells as the number of cells
+# It can be RC, ncells, none or the name of any quantitative column
+# in the @meta.data
 # @param tileSize The size of the tiles in the bigwig file
 # @param minCells The minimum of cells in a group to be exported
 # @param cutoff The maximum number of fragment in a given tile
@@ -2264,7 +2264,7 @@ ExportGroupBW  <- function(
   assay = NULL,
   group.by = NULL,
   idents = NULL,
-  normMethod = "nCount_peaks",
+  normMethod = "RC",
   tileSize = 100,
   minCells = 5,
   cutoff = NULL,
@@ -2313,7 +2313,7 @@ ExportGroupBW  <- function(
        
     #Column to normalized by
     if(!is.null(normMethod)){
-      if (normMethod == 'ncells'){
+      if (tolower(normMethod) %in% ('rc', 'ncells', 'none')){
         normBy <- normMethod
       } else{
         normBy <- object[[normMethod, drop=FALSE]]
@@ -2363,8 +2363,8 @@ ExportGroupBW  <- function(
 # or ncells as number of cells normalization
 # @param tileSize The size of the tiles in the bigwig file
 # @param normMethod Normalization method for the biwig files
-# It can be the name of any quantitative column in the @meta.data
-# or ncells as the number of cells
+# It can be RC, ncells, none or the name of any quantitative column
+# in the @meta.data
 # @param cutoff The maximum number of fragment in a given tile
 # @param outdir The output directory for bigwig file
 # Also used as output directory for SlitFragment function
@@ -2379,7 +2379,7 @@ CreateBWGroup <- function(groupNamei, availableChr, chromLengths, tiles, normBy,
   fragi <- rtracklayer::import(paste0(outdir, .Platform$file.sep, groupNamei, ".bed"),format = "bed")
 
   cellGroupi <- unique(fragi$name)
-
+  
   #Open the writting bigwig file
   covFile <- file.path(outdir, paste0(groupNamei, "-TileSize-",tileSize,"-normMethod-",normMethod,".bw"))
 
@@ -2420,11 +2420,13 @@ CreateBWGroup <- function(groupNamei, availableChr, chromLengths, tiles, normBy,
 
       tilesk$reads <- mat
 
-      #Normalization of counts by the sum of readsintss for each cells in group
+      #Normalization
       if(!is.null(normMethod)){
-        if(normMethod == "ncells"){
+        if(tolower(normMethod) == "rc"){
+          tilesk$reads <- tilesk$reads * 10^4 / length(fragi$name)
+        }else if(tolower(normMethod) == "ncells"){
           tilesk$reads <- tilesk$reads / length(cellGroupi)
-        }else if(tolower(normMethod) %in% c("none")){
+        }else if(tolower(normMethod) == "none"){
         }else{
           if(!is.null(normBy)){
             tilesk$reads <- tilesk$reads * 10^4 / sum(normBy[cellGroupi, 1])

From 14171951014ddca15ca016dcc131f4949818a77b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bastien=20Herv=C3=A9?= <bastienherve61@gmail.com>
Date: Thu, 4 May 2023 16:32:19 +0200
Subject: [PATCH 05/34] Update utilities.R

Roxygen documentation and tests
---
 R/utilities.R | 105 +++++++++++++++++++++++++++++---------------------
 1 file changed, 62 insertions(+), 43 deletions(-)

diff --git a/R/utilities.R b/R/utilities.R
index dacd9227..b91297f2 100644
--- a/R/utilities.R
+++ b/R/utilities.R
@@ -2238,29 +2238,36 @@ SparseSpearmanCor <- function(X, Y = NULL, cov = FALSE) {
   return(qlcMatrix::corSparse(X = rankX, Y = rankY, cov = cov))
 }
 
-# Export bigwig file for each group of bed file present in outdir
-# @param object The seurat object
-# @param assay The assay of the fragment file
-# @param group.by The metadata used to split the fragment file
-# @param idents The idents from the group.by to be exported
-# @param normMethod Normalization method for the biwig files
-# It can be RC, ncells, none or the name of any quantitative column
-# in the @meta.data
-# @param tileSize The size of the tiles in the bigwig file
-# @param minCells The minimum of cells in a group to be exported
-# @param cutoff The maximum number of fragment in a given tile
-# @param chromosome A chromosomes vector to be exported, standard
-# chromosomes can be fetched via standardChromosomes()
-# @param threads Number of threads
-# @param outdir The output directory for bigwig file
-# Also used as output directory for SlitFragment function
-# @param verbose Display messages
+#' Export bigwig file for each group of bed file present in outdir
+#'
+#' @param object The seurat object
+#' @param assay The assay of the fragment file
+#' @param group.by The metadata used to split the fragment file
+#' @param idents The idents from the group.by to be exported
+#' @param normMethod Normalization method for the biwig files. Deafult 'RC'.
+'RC' will divide the number of fragments in a tile by the number of fragments in the group. A scaling factor of 10^4 will be applied
+'ncells' will divide the number of fragments in a tile by the number of cell in the group.
+'none' will apply no normalization method.
+A vector of values for each cell can also be passed as a meta.data column name. A scaling factor of 10^4 will be applied
+#' @param tileSize The size of the tiles in the bigwig file
+#' @param minCells The minimum of cells in a group to be exported
+#' @param cutoff The maximum number of fragment in a given tile
+#' @param chromosome A chromosomes vector to be exported
+#' @param outdir The output directory for bigwig file
+#' @param verbose Display messages
+#'
 #' @importFrom GenomicRanges seqlengths GRanges slidingWindows
 #' @importFrom future plan
 #' @importFrom future.apply future_lapply
-
+#' @importFrom pbapply pbapply
+#'
+#' @return
+#' @export
+#'
+#' @examples
+#' ExportGroupBW(object, assay = "peaks", group.by = "seurat_clusters", idents=NULL, normMethod = "RC", tileSize = 100, minCells = 5, cutoff = NULL, chromosome = NULL, outdir = getwd(), verbose=TRUE)
 ExportGroupBW  <- function(
-  object = NULL,
+  object,
   assay = NULL,
   group.by = NULL,
   idents = NULL,
@@ -2269,24 +2276,27 @@ ExportGroupBW  <- function(
   minCells = 5,
   cutoff = NULL,
   chromosome = NULL,
-  threads = NULL,
   outdir = NULL,
   verbose=TRUE
   ){
   
+    #Check if temporary directory exist
+    if (!dir.exists(outdir)){
+      dir.create(outdir)
+    }
+  
     if (!requireNamespace("rtracklayer", quietly = TRUE)) { 
       message("Please install rtracklayer. http://www.bioconductor.org/packages/rtracklayer/") 
       return(NULL) 
-    } 
+    }
   
     assay <- assay %||% DefaultAssay(object = object)
     DefaultAssay(object = object) <- assay
-  
+      
     group.by <- group.by %||% 'ident'
     Idents(object = object) <- group.by
   
-    idents <- idents %||% levels(object = object)
-    levels(object = object) <- idents
+    idents <- idents %||% levels(object)
   
     GroupsNames <- names(table(object[[group.by]])[table(object[[group.by]]) > minCells])
     GroupsNames <- GroupsNames[GroupsNames %in% idents]
@@ -2295,6 +2305,7 @@ ExportGroupBW  <- function(
     lapply(GroupsNames, function(x){
       if (file.exists(paste0(outdir, .Platform$file.sep, x, ".bed"))){
         message(sprintf("The group \"%s\" is already present in the destination folder and will be overwritten !",x))
+        file.remove(paste0(outdir, .Platform$file.sep, x, ".bed"))
       }
     })      
       
@@ -2313,7 +2324,7 @@ ExportGroupBW  <- function(
        
     #Column to normalized by
     if(!is.null(normMethod)){
-      if (tolower(normMethod) %in% ('rc', 'ncells', 'none')){
+      if (tolower(normMethod) %in% c('rc', 'ncells', 'none')){
         normBy <- normMethod
       } else{
         normBy <- object[[normMethod, drop=FALSE]]
@@ -2328,7 +2339,7 @@ ExportGroupBW  <- function(
     availableChr <- names(seqlengths(object))
     chromLengths <- seqlengths(object)
     chromSizes <- GRanges(seqnames = availableChr, IRanges(start = rep(1, length(availableChr)), end = as.numeric(chromLengths)))
-
+    
     if (verbose) {
       message("Creation of tiles")
     }
@@ -2346,33 +2357,41 @@ ExportGroupBW  <- function(
       mylapply <- future_lapply 
     } else { 
       mylapply <- ifelse(test = verbose, yes = pblapply, no = lapply) 
-    } 
-  
+    }
+    
     covFiles <- mylapply(GroupsNames, CreateBWGroup, availableChr, chromLengths, tiles, normBy, tileSize, normMethod, cutoff, outdir)
 
     covFiles
 
   }
 
-# Helper function for ExportGroupBW
-# @param groupNamei The group to be exported
-# @param availableChr Chromosomes to be processed
-# @param chromLengths Chromosomes lengths
-# @param tiles The tiles object
-# @param normBy A vector of values to normalized the cells by
-# or ncells as number of cells normalization
-# @param tileSize The size of the tiles in the bigwig file
-# @param normMethod Normalization method for the biwig files
-# It can be RC, ncells, none or the name of any quantitative column
-# in the @meta.data
-# @param cutoff The maximum number of fragment in a given tile
-# @param outdir The output directory for bigwig file
-# Also used as output directory for SlitFragment function
+#' Helper function for ExportGroupBW
+#'
+#' @param groupNamei The group to be exported
+#' @param availableChr Chromosomes to be processed
+#' @param chromLengths Chromosomes lengths
+#' @param tiles The tiles object
+#' @param normBy A vector of values to normalized the cells by
+#' @param tileSize The size of the tiles in the bigwig file
+#' @param normMethod Normalization method for the biwig files
+'RC' will divide the number of fragments in a tile by the number of fragments in the group. A scaling factor of 10^4 will be applied
+'ncells' will divide the number of fragments in a tile by the number of cell in the group.
+'none' will apply no normalization method.
+A vector of values for each cell can also be passed as a meta.data column name. A scaling factor of 10^4 will be applied
+#' @param cutoff The maximum number of fragment in a given tile
+#' @param outdir The output directory for bigwig file
+#'
 #' @importFrom rtracklayer import export.bw
 #' @importFrom GenomicRanges seqnames seqlengths GRanges coverage
 #' @importFrom BiocGenerics which
 #' @importFrom S4Vectors match
 #' @importFrom Matrix sparseMatrix rowSums
+#'
+#' @return The names of the exported files
+#' @export
+#'
+#' @examples
+#' CreateBWGroup(group, availableChr, chromLengths, tiles, normBy, tileSize, normMethod, cutoff, getwd())
 CreateBWGroup <- function(groupNamei, availableChr, chromLengths, tiles, normBy, tileSize, normMethod, cutoff, outdir){
 
   #Read the fragments file associated to the group
@@ -2407,7 +2426,7 @@ CreateBWGroup <- function(groupNamei, availableChr, chromLengths, tiles, normBy,
       mat <- Matrix::sparseMatrix(
         i = c(trunc(start(fragik) / tileSize), trunc(end(fragik) / tileSize)) + 1,
         j = as.vector(c(matchID, matchID)),
-        x = rep(1,  2*length(fragik)),
+        x = rep(1, 2*length(fragik)),
         dims = c(nTiles, length(cellGroupi)))
 
       #Max count for a cells in a tile is set to cutoff

From 6309c3bd2969e81b3856d0ed782ec2d7bfa2bdaf Mon Sep 17 00:00:00 2001
From: timoast <4591688+timoast@users.noreply.github.com>
Date: Fri, 23 Jun 2023 17:19:03 +0800
Subject: [PATCH 06/34] Update function documentation

---
 R/utilities.R | 608 +++++++++++++++++++++++++-------------------------
 1 file changed, 304 insertions(+), 304 deletions(-)

diff --git a/R/utilities.R b/R/utilities.R
index cb3d23a9..545d1e13 100644
--- a/R/utilities.R
+++ b/R/utilities.R
@@ -28,24 +28,24 @@ NULL
 #' @export
 #' @concept utilities
 AddChromatinModule <- function(
-  object,
-  features,
-  genome,
-  assay = NULL,
-  verbose = TRUE,
-  ...
+    object,
+    features,
+    genome,
+    assay = NULL,
+    verbose = TRUE,
+    ...
 ) {
   assay <- SetIfNull(x = assay, y = DefaultAssay(object = object))
   if (!inherits(x = object[[assay]], what = "ChromatinAssay")) {
     stop("The requested assay is not a ChromatinAssay.")
   }
-
+  
   # first find index of each feature
   feat.idx <- sapply(X = features, FUN = fmatch, rownames(x = object[[assay]]))
   j <- sapply(X = seq_along(along.with = features), FUN = function(x) {
     rep(x = x, length(x = features[[x]]))
   })
-
+  
   # construct sparse matrix with features
   mat <- sparseMatrix(
     i = unlist(x = feat.idx, use.names = FALSE),
@@ -55,7 +55,7 @@ AddChromatinModule <- function(
   )
   rownames(x = mat) <- rownames(x = object[[assay]])
   colnames(x = mat) <- names(x = features)
-
+  
   # run chromVAR
   cv <- RunChromVAR(
     object = object[[assay]],
@@ -64,7 +64,7 @@ AddChromatinModule <- function(
     verbose = verbose,
     ...
   )
-
+  
   # add module scores to metadata
   chromvar.data <- GetAssayData(object = cv, slot = "data")
   object <- AddMetaData(
@@ -92,10 +92,10 @@ globalVariables(names = c("group", "readcount"), package = "Signac")
 #' @examples
 #' AverageCounts(atac_small)
 AverageCounts <- function(
-  object,
-  assay = NULL,
-  group.by = NULL,
-  verbose = TRUE
+    object,
+    assay = NULL,
+    group.by = NULL,
+    verbose = TRUE
 ) {
   assay <- SetIfNull(x = assay, y = DefaultAssay(object = object))
   if (is.null(x = group.by)) {
@@ -135,11 +135,11 @@ AverageCounts <- function(
 #' @importFrom Matrix rowSums
 #' @return Returns a vector of peak names
 AccessiblePeaks <- function(
-  object,
-  assay = NULL,
-  idents = NULL,
-  cells = NULL,
-  min.cells = 10
+    object,
+    assay = NULL,
+    idents = NULL,
+    cells = NULL,
+    min.cells = 10
 ) {
   assay <- SetIfNull(x = assay, y = DefaultAssay(object = object))
   cells <- SetIfNull(x = cells, y = WhichCells(object, idents = idents))
@@ -165,8 +165,8 @@ AccessiblePeaks <- function(
 #' @examples
 #' CellsPerGroup(atac_small)
 CellsPerGroup <- function(
-  object,
-  group.by = NULL
+    object,
+    group.by = NULL
 ) {
   if (is.null(x = group.by)) {
     cellgroups <- Idents(object = object)
@@ -207,10 +207,10 @@ CellsPerGroup <- function(
 #' )
 #' }
 ClosestFeature <- function(
-  object,
-  regions,
-  annotation = NULL,
-  ...
+    object,
+    regions,
+    annotation = NULL,
+    ...
 ) {
   if (!is(object = regions, class2 = 'GRanges')) {
     regions <- StringToGRanges(regions = regions, ...)
@@ -290,16 +290,16 @@ ClosestFeature <- function(
 #' Fragments(atac_small) <- fragments
 #' GeneActivity(atac_small)
 GeneActivity <- function(
-  object,
-  assay = NULL,
-  features = NULL,
-  extend.upstream = 2000,
-  extend.downstream = 0,
-  biotypes = "protein_coding",
-  max.width = 500000,
-  process_n = 2000,
-  gene.id = FALSE,
-  verbose = TRUE
+    object,
+    assay = NULL,
+    features = NULL,
+    extend.upstream = 2000,
+    extend.downstream = 0,
+    biotypes = "protein_coding",
+    max.width = 500000,
+    process_n = 2000,
+    gene.id = FALSE,
+    verbose = TRUE
 ) {
   if (!is.null(x = features)) {
     if (length(x = features) == 0) {
@@ -334,7 +334,7 @@ GeneActivity <- function(
       stop("No genes remaining after filtering for requested biotypes")
     }
   }
-
+  
   # filter genes if provided
   if (!is.null(x = features)) {
     transcripts <- transcripts[transcripts$gene_name %in% features]
@@ -349,14 +349,14 @@ GeneActivity <- function(
       stop("No genes remaining after filtering for max.width")
     }
   }
-
+  
   # extend to include promoters
   transcripts <- Extend(
     x = transcripts,
     upstream = extend.upstream,
     downstream = extend.downstream
   )
-
+  
   # quantify
   frags <- Fragments(object = object[[assay]])
   if (length(x = frags) == 0) {
@@ -375,7 +375,7 @@ GeneActivity <- function(
   names(x = gene.key) <- GRangesToString(grange = transcripts)
   rownames(x = counts) <- as.vector(x = gene.key[rownames(x = counts)])
   counts <- counts[rownames(x = counts) != "", ]
-
+  
   return(counts)
 }
 
@@ -395,10 +395,10 @@ GeneActivity <- function(
 #' @concept utilities
 #' @export
 GetGRangesFromEnsDb <- function(
-  ensdb,
-  standard.chromosomes = TRUE,
-  biotypes = c("protein_coding", "lincRNA", "rRNA", "processed_transcript"),
-  verbose = TRUE
+    ensdb,
+    standard.chromosomes = TRUE,
+    biotypes = c("protein_coding", "lincRNA", "rRNA", "processed_transcript"),
+    verbose = TRUE
 ) {
   if (!requireNamespace("biovizBase", quietly = TRUE)) {
     stop("Please install biovizBase\n",
@@ -409,15 +409,15 @@ GetGRangesFromEnsDb <- function(
   if (standard.chromosomes) {
     whole.genome <- keepStandardChromosomes(whole.genome, pruning.mode = "coarse")
   }
-
+  
   # extract genes from each chromosome
   my_lapply <- ifelse(test = verbose, yes = pblapply, no = lapply)
   tx <- my_lapply(X = seq_along(whole.genome), FUN = function(x){
-        suppressMessages(expr = biovizBase::crunch(
-          obj = ensdb,
-          which = whole.genome[x],
-          columns = c("tx_id", "gene_name", "gene_id", "gene_biotype")))
-      })
+    suppressMessages(expr = biovizBase::crunch(
+      obj = ensdb,
+      which = whole.genome[x],
+      columns = c("tx_id", "gene_name", "gene_id", "gene_biotype")))
+  })
   
   # combine
   tx <- do.call(what = c, args = tx)
@@ -486,12 +486,12 @@ GetTSSPositions <- function(ranges, biotypes = "protein_coding") {
 #'   assay.2 = 'bins'
 #' )
 GetIntersectingFeatures <- function(
-  object.1,
-  object.2,
-  assay.1 = NULL,
-  assay.2 = NULL,
-  distance = 0,
-  verbose = TRUE
+    object.1,
+    object.2,
+    assay.1 = NULL,
+    assay.2 = NULL,
+    distance = 0,
+    verbose = TRUE
 ) {
   assay.1 <- SetIfNull(x = assay.1, y = DefaultAssay(object = object.1))
   assay.2 <- SetIfNull(x = assay.2, y = DefaultAssay(object = object.2))
@@ -591,10 +591,10 @@ GRangesToString <- function(grange, sep = c("-", "-")) {
 #' @examples
 #' Extend(x = blacklist_hg19, upstream = 100, downstream = 100)
 Extend <- function(
-  x,
-  upstream = 0,
-  downstream = 0,
-  from.midpoint = FALSE
+    x,
+    upstream = 0,
+    downstream = 0,
+    from.midpoint = FALSE
 ) {
   if (any(strand(x = x) == "*")) {
     warning("'*' ranges were treated as '+'")
@@ -683,10 +683,10 @@ GetCellsInRegion <- function(tabix, region, cells = NULL) {
 #' )
 #' }
 CountsInRegion <- function(
-  object,
-  assay,
-  regions,
-  ...
+    object,
+    assay,
+    regions,
+    ...
 ) {
   if (!is(object = object[[assay]], class2 = "ChromatinAssay")) {
     stop("Must supply a ChromatinAssay")
@@ -724,10 +724,10 @@ CountsInRegion <- function(
 #' )
 #' }
 FractionCountsInRegion <- function(
-  object,
-  regions,
-  assay = NULL,
-  ...
+    object,
+    regions,
+    assay = NULL,
+    ...
 ) {
   assay <- SetIfNull(x = assay, y = DefaultAssay(object = object))
   reads.in.region <- CountsInRegion(
@@ -772,12 +772,12 @@ FractionCountsInRegion <- function(
 #' "chr1-762106-763359","chr1-779589-780271")
 #' IntersectMatrix(matrix = counts, regions = blacklist_hg19)
 IntersectMatrix <- function(
-  matrix,
-  regions,
-  invert = FALSE,
-  sep = c("-", "-"),
-  verbose = TRUE,
-  ...
+    matrix,
+    regions,
+    invert = FALSE,
+    sep = c("-", "-"),
+    verbose = TRUE,
+    ...
 ) {
   if (is(object = regions, class2 = "character")) {
     regions <- StringToGRanges(regions = regions, sep = sep)
@@ -880,12 +880,12 @@ LookupGeneCoords <- function(object, gene, assay = NULL) {
 #'   n = 10
 #' )
 MatchRegionStats <- function(
-  meta.feature,
-  query.feature,
-  features.match = c("GC.percent"),
-  n = 10000,
-  verbose = TRUE,
-  ...
+    meta.feature,
+    query.feature,
+    features.match = c("GC.percent"),
+    n = 10000,
+    verbose = TRUE,
+    ...
 ) {
   if (!inherits(x = meta.feature, what = 'data.frame')) {
     stop("meta.feature should be a data.frame")
@@ -997,11 +997,11 @@ UnifyPeaks <- function(object.list, mode = "reduce") {
 #' @examples
 #' SubsetMatrix(mat = volcano)
 SubsetMatrix <- function(
-  mat,
-  min.rows = 1,
-  min.cols = 1,
-  max.row.val = 10,
-  max.col.val = NULL
+    mat,
+    min.rows = 1,
+    min.cols = 1,
+    max.row.val = 10,
+    max.col.val = NULL
 ) {
   rowcount <- rowSums(mat > 0)
   colcount <- colSums(mat > 0)
@@ -1053,10 +1053,10 @@ AddMissingCells <- function(x, cells) {
 #' @importFrom SeuratObject DefaultAssay GetAssayData
 #' @importFrom Matrix Diagonal tcrossprod rowSums
 AverageCountMatrix <- function(
-  object,
-  assay = NULL,
-  group.by = NULL,
-  idents = NULL
+    object,
+    assay = NULL,
+    group.by = NULL,
+    idents = NULL
 ) {
   assay = SetIfNull(x = assay, y = DefaultAssay(object = object))
   countmatrix <- GetAssayData(object = object[[assay]], slot = "counts")
@@ -1242,12 +1242,12 @@ ExtractFragments <- function(fragments, n = NULL, verbose = TRUE) {
 # convert region argument to genomic coordinates
 # region can be a string, name of a gene, or GRanges object
 FindRegion <- function(
-  object,
-  region,
-  sep = c("-", "-"),
-  assay = NULL,
-  extend.upstream = 0,
-  extend.downstream = 0
+    object,
+    region,
+    sep = c("-", "-"),
+    assay = NULL,
+    extend.upstream = 0,
+    extend.downstream = 0
 ) {
   if (!is(object = region, class2 = "GRanges")) {
     # first try to convert to coordinates, if not lookup gene
@@ -1298,16 +1298,16 @@ FindRegion <- function(
 #
 # @return Returns a data frame
 GetReadsInRegion <- function(
-  cellmap,
-  region,
-  tabix.file,
-  cells = NULL,
-  verbose = TRUE,
-  ...
+    cellmap,
+    region,
+    tabix.file,
+    cells = NULL,
+    verbose = TRUE,
+    ...
 ) {
   file.to.object <- names(x = cellmap)
   names(x = file.to.object) <- cellmap
-
+  
   if (verbose) {
     message("Extracting reads in requested region")
   }
@@ -1362,9 +1362,9 @@ GetReadsInRegion <- function(
 # @return Returns a named vector
 #' @importFrom SeuratObject Idents
 GetGroups <- function(
-  object,
-  group.by,
-  idents
+    object,
+    group.by,
+    idents
 ) {
   if (is.null(x = group.by)) {
     obj.groups <- Idents(object = object)
@@ -1414,11 +1414,11 @@ MergeMatrixParts <- function(mat.list, new.rownames) {
 #' @importFrom Rsamtools TabixFile
 #' @importFrom GenomeInfoDb keepSeqlevels
 MultiGetReadsInRegion <- function(
-  object,
-  region,
-  fragment.list = NULL,
-  assay = NULL,
-  ...
+    object,
+    region,
+    fragment.list = NULL,
+    assay = NULL,
+    ...
 ) {
   if (inherits(x = object, what = "Seurat")) {
     # pull the assay
@@ -1471,11 +1471,11 @@ MultiGetReadsInRegion <- function(
 #' @importMethodsFrom GenomicRanges width start end
 # @return Returns a sparse matrix
 SingleFileCutMatrix <- function(
-  cellmap,
-  region,
-  cells = NULL,
-  tabix.file,
-  verbose = TRUE
+    cellmap,
+    region,
+    cells = NULL,
+    tabix.file,
+    verbose = TRUE
 ) {
   # if multiple regions supplied, must be the same width
   cells <- SetIfNull(x = cells, y = names(x = cellmap))
@@ -1508,7 +1508,7 @@ SingleFileCutMatrix <- function(
     )
     cut.df <- cut.df[
       (cut.df$position > 0) & (cut.df$position <= width(x = region)[[1]]),
-      ]
+    ]
     cell.vector <- seq_along(along.with = cells)
     names(x = cell.vector) <- cells
     cell.matrix.info <- cell.vector[cut.df$cell]
@@ -1541,12 +1541,12 @@ SingleFileCutMatrix <- function(
 #' @importFrom Rsamtools TabixFile seqnamesTabix
 #' @importFrom GenomeInfoDb keepSeqlevels
 CutMatrix <- function(
-  object,
-  region,
-  group.by = NULL,
-  assay = NULL,
-  cells = NULL,
-  verbose = TRUE
+    object,
+    region,
+    group.by = NULL,
+    assay = NULL,
+    cells = NULL,
+    verbose = TRUE
 ) {
   # run SingleFileCutMatrix for each fragment file and combine results
   assay <- SetIfNull(x = assay, y = DefaultAssay(object = object))
@@ -1603,13 +1603,13 @@ CutMatrix <- function(
 #' @importFrom SeuratObject DefaultAssay
 #' @importFrom GenomeInfoDb keepSeqlevels
 MultiRegionCutMatrix <- function(
-  object,
-  regions,
-  group.by = NULL,
-  fragments = NULL,
-  assay = NULL,
-  cells = NULL,
-  verbose = FALSE
+    object,
+    regions,
+    group.by = NULL,
+    fragments = NULL,
+    assay = NULL,
+    cells = NULL,
+    verbose = FALSE
 ) {
   if (inherits(x = object, what = "Seurat")) {
     assay <- SetIfNull(x = assay, y = DefaultAssay(object = object))
@@ -1666,11 +1666,11 @@ MultiRegionCutMatrix <- function(
 # @param verbose Display messages
 #' @importMethodsFrom GenomicRanges strand
 CreateRegionPileupMatrix <- function(
-  object,
-  regions,
-  assay = NULL,
-  cells = NULL,
-  verbose = TRUE
+    object,
+    regions,
+    assay = NULL,
+    cells = NULL,
+    verbose = TRUE
 ) {
   if (length(x = regions) == 0) {
     stop("No regions supplied")
@@ -1679,7 +1679,7 @@ CreateRegionPileupMatrix <- function(
   on_plus <- strand(x = regions) == "+" | strand(x = regions) == "*"
   plus.strand <- regions[on_plus, ]
   minus.strand <- regions[!on_plus, ]
-
+  
   # get cut matrices for each strand
   if (verbose) {
     message("Finding + strand cut sites")
@@ -1701,7 +1701,7 @@ CreateRegionPileupMatrix <- function(
     cells = cells,
     verbose = FALSE
   )
-
+  
   # reverse minus strand and add together
   if (is.null(x = cut.matrix.plus)) {
     full.matrix <- cut.matrix.minus[, rev(x = colnames(x = cut.matrix.minus))]
@@ -1737,12 +1737,12 @@ CreateRegionPileupMatrix <- function(
 # @param scale.factor Scaling factor to use. If NULL (default), will use the
 # median normalization factor for all the groups.
 ApplyMatrixByGroup <- function(
-  mat,
-  groups,
-  fun,
-  normalize = TRUE,
-  group.scale.factors = NULL,
-  scale.factor = NULL
+    mat,
+    groups,
+    fun,
+    normalize = TRUE,
+    group.scale.factors = NULL,
+    scale.factor = NULL
 ) {
   if (normalize) {
     if (is.null(x = group.scale.factors) | is.null(x = scale.factor)) {
@@ -1755,13 +1755,13 @@ ApplyMatrixByGroup <- function(
   }
   ngroup <- length(x = all.groups)
   npos <- ncol(x = mat)
-
+  
   group <- unlist(
     x = lapply(X = all.groups, FUN = function(x) rep(x, npos))
   )
   position <- rep(x = as.numeric(x = colnames(x = mat)), ngroup)
   count <- vector(mode = "numeric", length = npos * ngroup)
-
+  
   for (i in seq_along(along.with = all.groups)) {
     grp <- all.groups[[i]]
     if (is.na(x = grp)) {
@@ -1776,13 +1776,13 @@ ApplyMatrixByGroup <- function(
     }
     count[((i - 1) * npos + 1):((i * npos))] <- totals
   }
-
+  
   # construct dataframe
   coverages <- data.frame(
     "group" = group, "position" = position, "count" = count,
     stringsAsFactors = FALSE
   )
-
+  
   if (normalize) {
     scale.factor <- SetIfNull(
       x = scale.factor, y = median(x = group.scale.factors)
@@ -1911,12 +1911,12 @@ IsMatrixEmpty <- function(x) {
 # information
 GetRowsToMerge <- function(assay.list, all.ranges, reduced.ranges) {
   revmap <- as.vector(x = reduced.ranges$revmap)
-
+  
   # get indices of ranges that changed
   revmap.lengths <- sapply(X = revmap, FUN = length)
   changed.ranges <- which(x = revmap.lengths > 1)
   grange.string <- GRangesToString(grange = reduced.ranges[changed.ranges])
-
+  
   # preallocate
   offsets <- list()
   results <- list()
@@ -1935,7 +1935,7 @@ GetRowsToMerge <- function(assay.list, all.ranges, reduced.ranges) {
     results[['matrix']][[i]] <- matrix.indices
     results[['grange']][[i]] <- granges
   }
-
+  
   # find sets of ranges for each dataset
   counter <- vector(mode = "numeric", length = length(x = assay.list))
   for (x in seq_along(along.with = changed.ranges)) {
@@ -1971,16 +1971,16 @@ GetRowsToMerge <- function(assay.list, all.ranges, reduced.ranges) {
 #' @importFrom Matrix rowSums
 #' @importMethodsFrom Matrix t
 MergeOverlappingRows <- function(
-  mergeinfo,
-  assay.list,
-  slot = "counts",
-  verbose = TRUE
+    mergeinfo,
+    assay.list,
+    slot = "counts",
+    verbose = TRUE
 ) {
   merge.counts <- list()
   for (i in seq_along(along.with = assay.list)) {
     # get count matrix
     counts <- GetAssayData(object = assay.list[[i]], slot = slot)
-
+    
     if (nrow(x = counts) == 0) {
       # no counts, only data
       # skip row merge and return empty counts matrices
@@ -1992,15 +1992,15 @@ MergeOverlappingRows <- function(
       )
       return(merge.counts)
     }
-
+    
     # transpose for faster access since matrix is column major
     counts <- t(x = counts)
-
+    
     # get rows to merge
     mrows <- mergeinfo$matrix[[i]]
     new.rownames <- mergeinfo$grange[[i]]
     nrep <- rle(x = new.rownames)
-
+    
     # allocate
     todelete <- c()
     newmat <- vector(
@@ -2058,13 +2058,13 @@ MergeOverlappingRows <- function(
     to.rename.names <- to.rename.names[1:idx.counter]
     newmat <- newmat[1:(y - 1)]
     newmat.names <- newmat.names[1:(y - 1)]
-
+    
     # transpose back
     counts <- t(x = counts)
-
+    
     # rename matrix rows that weren't merged
     rownames(counts)[to.rename.idx] <- to.rename.names
-
+    
     if (y == 1) {
       # no rows were merged, can return counts
       merge.counts[[i]] <- counts
@@ -2084,12 +2084,12 @@ MergeOverlappingRows <- function(
       merged.mat <- Reduce(f = rbind, x = newmat)
       rownames(merged.mat) <- newmat.names
       merged.mat <- as(object = merged.mat, Class = "CsparseMatrix")
-
+      
       # remove rows from count matrix that were merged
       mat.rows <- seq_len(length.out = nrow(x = counts))
       tokeep <- setdiff(mat.rows, todelete)
       counts <- counts[tokeep, ]
-
+      
       # add new merged rows to counts
       counts <- rbind(counts, merged.mat)
       merge.counts[[i]] <- counts
@@ -2231,8 +2231,8 @@ SparsifiedRanks <- function(X){
     x = lapply(
       X = seq_along(col_lst),
       FUN = function(i) rank(x = col_lst[[i]]) + offsets[i]
-      )
     )
+  )
   ## Create template rank matrix
   X.ranks <- X
   X.ranks@x <- sparsified_ranks
@@ -2248,25 +2248,27 @@ SparseSpearmanCor <- function(X, Y = NULL, cov = FALSE) {
   if (is.null(Y)){
     # Calculate pearson correlation on rank matrices
     return (qlcMatrix::corSparse(X = rankX, cov = cov))
-    }
+  }
   rankY <- SparsifiedRanks(X = Y)
   return(qlcMatrix::corSparse(X = rankX, Y = rankY, cov = cov))
 }
 
-#' Export bigwig file for each group of bed file present in outdir
-#'
-#' @param object The seurat object
-#' @param assay The assay of the fragment file
-#' @param group.by The metadata used to split the fragment file
-#' @param idents The idents from the group.by to be exported
-#' @param normMethod Normalization method for the biwig files. Deafult 'RC'.
-'RC' will divide the number of fragments in a tile by the number of fragments in the group. A scaling factor of 10^4 will be applied
-'ncells' will divide the number of fragments in a tile by the number of cell in the group.
-'none' will apply no normalization method.
-A vector of values for each cell can also be passed as a meta.data column name. A scaling factor of 10^4 will be applied
+#' Export bigwig files for groups of cells
+#'
+#' @param object A Seurat object
+#' @param assay Name of assay to use
+#' @param group.by The metadata variable used to group the cells
+#' @param idents Identities to include (defined by group.by parameter)
+#' @param normMethod Normalization method for the bigwig files. Deafult 'RC'.
+#' 'RC' will divide the number of fragments in a tile by the total number of
+#' fragments in the group. A scaling factor of 10^4 will be applied. 
+#' 'ncells' will divide the number of fragments in a tile by the number of cell
+#' in the group. 'none' will apply no normalization method. 
+#' A vector of values for each cell can also be passed as a metadata column
+#' name. A scaling factor of 10^4 will be applied
 #' @param tileSize The size of the tiles in the bigwig file
 #' @param minCells The minimum of cells in a group to be exported
-#' @param cutoff The maximum number of fragment in a given tile
+#' @param cutoff The maximum number of fragments in a given genomic tile
 #' @param chromosome A chromosomes vector to be exported
 #' @param outdir The output directory for bigwig file
 #' @param verbose Display messages
@@ -2280,180 +2282,178 @@ A vector of values for each cell can also be passed as a meta.data column name.
 #' @export
 #'
 #' @examples
-#' ExportGroupBW(object, assay = "peaks", group.by = "seurat_clusters", idents=NULL, normMethod = "RC", tileSize = 100, minCells = 5, cutoff = NULL, chromosome = NULL, outdir = getwd(), verbose=TRUE)
+#' \dontrun{
+#' ExportGroupBW(object, assay = "peaks")
+#' }
 ExportGroupBW  <- function(
-  object,
-  assay = NULL,
-  group.by = NULL,
-  idents = NULL,
-  normMethod = "RC",
-  tileSize = 100,
-  minCells = 5,
-  cutoff = NULL,
-  chromosome = NULL,
-  outdir = NULL,
-  verbose=TRUE
-  ){
+    object,
+    assay = NULL,
+    group.by = NULL,
+    idents = NULL,
+    normMethod = "RC",
+    tileSize = 100,
+    minCells = 5,
+    cutoff = NULL,
+    chromosome = NULL,
+    outdir = NULL,
+    verbose=TRUE
+){
   
-    #Check if temporary directory exist
-    if (!dir.exists(outdir)){
-      dir.create(outdir)
-    }
+  #Check if temporary directory exist
+  if (!dir.exists(outdir)){
+    dir.create(outdir)
+  }
   
-    if (!requireNamespace("rtracklayer", quietly = TRUE)) { 
-      message("Please install rtracklayer. http://www.bioconductor.org/packages/rtracklayer/") 
-      return(NULL) 
-    }
+  if (!requireNamespace("rtracklayer", quietly = TRUE)) { 
+    message("Please install rtracklayer. http://www.bioconductor.org/packages/rtracklayer/") 
+    return(NULL) 
+  }
   
-    assay <- assay %||% DefaultAssay(object = object)
-    DefaultAssay(object = object) <- assay
-      
-    group.by <- group.by %||% 'ident'
-    Idents(object = object) <- group.by
+  assay <- assay %||% DefaultAssay(object = object)
+  DefaultAssay(object = object) <- assay
   
-    idents <- idents %||% levels(object)
+  group.by <- group.by %||% 'ident'
+  Idents(object = object) <- group.by
   
-    GroupsNames <- names(table(object[[group.by]])[table(object[[group.by]]) > minCells])
-    GroupsNames <- GroupsNames[GroupsNames %in% idents]
+  idents <- idents %||% levels(object)
   
-    #Check if output files already exist
-    lapply(GroupsNames, function(x){
-      if (file.exists(paste0(outdir, .Platform$file.sep, x, ".bed"))){
-        message(sprintf("The group \"%s\" is already present in the destination folder and will be overwritten !",x))
-        file.remove(paste0(outdir, .Platform$file.sep, x, ".bed"))
-      }
-    })      
-      
-    #Splitting fragments file for each idents in group.by
-    SplitFragments(
-      object = object,
-      assay = assay,
-      group.by = group.by,
-      idents = idents,
-      outdir = outdir,
-      file.suffix = "",
-      append = TRUE,
-      buffer_length = 256L,
-      verbose = verbose
-    )
-       
-    #Column to normalized by
-    if(!is.null(normMethod)){
-      if (tolower(normMethod) %in% c('rc', 'ncells', 'none')){
-        normBy <- normMethod
-      } else{
-        normBy <- object[[normMethod, drop=FALSE]]
-      }
-    }
-    
-    #Get chromosome information
-    if(!is.null(chromosome)){
-      seqlevels(object) <- chromosome
-    }
-
-    availableChr <- names(seqlengths(object))
-    chromLengths <- seqlengths(object)
-    chromSizes <- GRanges(seqnames = availableChr, IRanges(start = rep(1, length(availableChr)), end = as.numeric(chromLengths)))
-    
-    if (verbose) {
-      message("Creation of tiles")
-    }
-    
-    #Create tiles for each chromosome, from GenomicRanges
-    tiles <- unlist(slidingWindows(chromSizes, width = tileSize, step = tileSize))
-    
-    if (verbose) {
-      message("Bigwig files generation at ", outdir)
+  GroupsNames <- names(table(object[[group.by]])[table(object[[group.by]]) > minCells])
+  GroupsNames <- GroupsNames[GroupsNames %in% idents]
+  
+  #Check if output files already exist
+  lapply(GroupsNames, function(x){
+    if (file.exists(paste0(outdir, .Platform$file.sep, x, ".bed"))){
+      message(sprintf("The group \"%s\" is already present in the destination folder and will be overwritten !",x))
+      file.remove(paste0(outdir, .Platform$file.sep, x, ".bed"))
     }
-        
-    #Run the creation of bigwig for each cellgroups
+  })      
   
-    if (nbrOfWorkers() > 1) { 
-      mylapply <- future_lapply 
-    } else { 
-      mylapply <- ifelse(test = verbose, yes = pblapply, no = lapply) 
+  #Splitting fragments file for each idents in group.by
+  SplitFragments(
+    object = object,
+    assay = assay,
+    group.by = group.by,
+    idents = idents,
+    outdir = outdir,
+    file.suffix = "",
+    append = TRUE,
+    buffer_length = 256L,
+    verbose = verbose
+  )
+  
+  #Column to normalized by
+  if(!is.null(normMethod)){
+    if (tolower(normMethod) %in% c('rc', 'ncells', 'none')){
+      normBy <- normMethod
+    } else{
+      normBy <- object[[normMethod, drop=FALSE]]
     }
-    
-    covFiles <- mylapply(GroupsNames, CreateBWGroup, availableChr, chromLengths, tiles, normBy, tileSize, normMethod, cutoff, outdir)
-
-    covFiles
-
   }
+  
+  #Get chromosome information
+  if(!is.null(chromosome)){
+    seqlevels(object) <- chromosome
+  }
+  
+  availableChr <- names(seqlengths(object))
+  chromLengths <- seqlengths(object)
+  chromSizes <- GRanges(seqnames = availableChr, IRanges(start = rep(1, length(availableChr)), end = as.numeric(chromLengths)))
+  
+  if (verbose) {
+    message("Creation of tiles")
+  }
+  
+  #Create tiles for each chromosome, from GenomicRanges
+  tiles <- unlist(slidingWindows(chromSizes, width = tileSize, step = tileSize))
+  
+  if (verbose) {
+    message("Bigwig files generation at ", outdir)
+  }
+  
+  #Run the creation of bigwig for each cellgroups
+  
+  if (nbrOfWorkers() > 1) { 
+    mylapply <- future_lapply 
+  } else { 
+    mylapply <- ifelse(test = verbose, yes = pblapply, no = lapply) 
+  }
+  
+  covFiles <- mylapply(GroupsNames, CreateBWGroup, availableChr, chromLengths, tiles, normBy, tileSize, normMethod, cutoff, outdir)
+  
+  covFiles
+  
+}
 
-#' Helper function for ExportGroupBW
-#'
-#' @param groupNamei The group to be exported
-#' @param availableChr Chromosomes to be processed
-#' @param chromLengths Chromosomes lengths
-#' @param tiles The tiles object
-#' @param normBy A vector of values to normalized the cells by
-#' @param tileSize The size of the tiles in the bigwig file
-#' @param normMethod Normalization method for the biwig files
-'RC' will divide the number of fragments in a tile by the number of fragments in the group. A scaling factor of 10^4 will be applied
-'ncells' will divide the number of fragments in a tile by the number of cell in the group.
-'none' will apply no normalization method.
-A vector of values for each cell can also be passed as a meta.data column name. A scaling factor of 10^4 will be applied
-#' @param cutoff The maximum number of fragment in a given tile
-#' @param outdir The output directory for bigwig file
-#'
+# Helper function for ExportGroupBW
+#
+# @param groupNamei The group to be exported
+# @param availableChr Chromosomes to be processed
+# @param chromLengths Chromosomes lengths
+# @param tiles The tiles object
+# @param normBy A vector of values to normalized the cells by
+# @param tileSize The size of the tiles in the bigwig file
+# @param normMethod Normalization method for the bigwig files
+# 'RC' will divide the number of fragments in a tile by the number of fragments
+# in the group. A scaling factor of 10^4 will be applied
+# 'ncells' will divide the number of fragments in a tile by the number of cell
+# in the group. 'none' will apply no normalization method. A vector of values
+# for each cell can also be passed as a meta.data column name. A scaling factor
+# of 10^4 will be applied
+# @param cutoff The maximum number of fragment in a given tile
+# @param outdir The output directory for bigwig file
+#
 #' @importFrom rtracklayer import export.bw
 #' @importFrom GenomicRanges seqnames seqlengths GRanges coverage
 #' @importFrom BiocGenerics which
 #' @importFrom S4Vectors match
 #' @importFrom Matrix sparseMatrix rowSums
-#'
-#' @return The names of the exported files
-#' @export
-#'
-#' @examples
-#' CreateBWGroup(group, availableChr, chromLengths, tiles, normBy, tileSize, normMethod, cutoff, getwd())
 CreateBWGroup <- function(groupNamei, availableChr, chromLengths, tiles, normBy, tileSize, normMethod, cutoff, outdir){
-
+  
   #Read the fragments file associated to the group
   fragi <- rtracklayer::import(paste0(outdir, .Platform$file.sep, groupNamei, ".bed"),format = "bed")
-
+  
   cellGroupi <- unique(fragi$name)
   
   #Open the writting bigwig file
   covFile <- file.path(outdir, paste0(groupNamei, "-TileSize-",tileSize,"-normMethod-",normMethod,".bw"))
-
+  
   covList <- lapply(seq_along(availableChr), function(k){
-
+    
     fragik <- fragi[seqnames(fragi) == availableChr[k],]
     tilesk <- tiles[BiocGenerics::which(S4Vectors::match(seqnames(tiles), availableChr[k], nomatch = 0) > 0)]
     
     if(length(fragik) == 0){
       tilesk$reads <- 0
-    #If fragments
+      #If fragments
     }else{
-
+      
       #N Tiles
       nTiles <- chromLengths[availableChr[k]] / tileSize
       #Add one tile if there is extra bases
       if (nTiles%%1 != 0) {
         nTiles <- trunc(nTiles) + 1
       }
-
+      
       #Create Sparse Matrix
       matchID <- S4Vectors::match(mcols(fragik)$name, cellGroupi)
-
+      
       #For each tiles of this chromosome, create start tile and end tile row, set the associated counts matching with the fragments
       mat <- Matrix::sparseMatrix(
         i = c(trunc(start(fragik) / tileSize), trunc(end(fragik) / tileSize)) + 1,
         j = as.vector(c(matchID, matchID)),
         x = rep(1, 2*length(fragik)),
         dims = c(nTiles, length(cellGroupi)))
-
+      
       #Max count for a cells in a tile is set to cutoff
       if(!is.null(cutoff)){
         mat@x[mat@x > cutoff] <- cutoff
       }
-
+      
       #Sums the cells
       mat <- Matrix::rowSums(mat)
-
+      
       tilesk$reads <- mat
-
+      
       #Normalization
       if(!is.null(normMethod)){
         if(tolower(normMethod) == "rc"){
@@ -2468,18 +2468,18 @@ CreateBWGroup <- function(groupNamei, availableChr, chromLengths, tiles, normBy,
         }
       }
     }
-
+    
     tilesk <- coverage(tilesk, weight = tilesk$reads)[[availableChr[k]]]
-
+    
     tilesk
-
+    
   })
-
+  
   names(covList) <- availableChr
-
+  
   covList <- as(covList, "RleList")
-
+  
   rtracklayer::export.bw(object = covList, con = covFile)
-
+  
   return(covFile)
 }
\ No newline at end of file

From 0d5eee5b3bd6fb2f5118494de14ed5304c398eb8 Mon Sep 17 00:00:00 2001
From: timoast <4591688+timoast@users.noreply.github.com>
Date: Fri, 23 Jun 2023 17:37:23 +0800
Subject: [PATCH 07/34] Reformat

---
 R/utilities.R | 193 ++++++++++++++++++++++++++------------------------
 1 file changed, 101 insertions(+), 92 deletions(-)

diff --git a/R/utilities.R b/R/utilities.R
index 545d1e13..4854086d 100644
--- a/R/utilities.R
+++ b/R/utilities.R
@@ -2297,38 +2297,31 @@ ExportGroupBW  <- function(
     chromosome = NULL,
     outdir = NULL,
     verbose=TRUE
-){
-  
-  #Check if temporary directory exist
+) {
+  # Check if temporary directory exist
   if (!dir.exists(outdir)){
     dir.create(outdir)
   }
-  
   if (!requireNamespace("rtracklayer", quietly = TRUE)) { 
     message("Please install rtracklayer. http://www.bioconductor.org/packages/rtracklayer/") 
     return(NULL) 
   }
-  
-  assay <- assay %||% DefaultAssay(object = object)
+  assay <- SetIfNull(x = assay, y = DefaultAssay(object = object))
   DefaultAssay(object = object) <- assay
-  
-  group.by <- group.by %||% 'ident'
+  group.by <- SetIfNull(x = group.by, y = 'ident')
   Idents(object = object) <- group.by
-  
-  idents <- idents %||% levels(object)
-  
-  GroupsNames <- names(table(object[[group.by]])[table(object[[group.by]]) > minCells])
+  idents <- SetIfNull(x = idents, y = levels(x = object))
+  GroupsNames <- names(x = table(object[[group.by]])[table(object[[group.by]]) > minCells])
   GroupsNames <- GroupsNames[GroupsNames %in% idents]
-  
-  #Check if output files already exist
-  lapply(GroupsNames, function(x){
-    if (file.exists(paste0(outdir, .Platform$file.sep, x, ".bed"))){
+  # Check if output files already exist
+  lapply(X = GroupsNames, FUN = function(x) {
+    fn <- paste0(outdir, .Platform$file.sep, x, ".bed")
+    if (file.exists(fn)) {
       message(sprintf("The group \"%s\" is already present in the destination folder and will be overwritten !",x))
-      file.remove(paste0(outdir, .Platform$file.sep, x, ".bed"))
+      file.remove(fn)
     }
   })      
-  
-  #Splitting fragments file for each idents in group.by
+  # Splitting fragments file for each idents in group.by
   SplitFragments(
     object = object,
     assay = assay,
@@ -2340,48 +2333,57 @@ ExportGroupBW  <- function(
     buffer_length = 256L,
     verbose = verbose
   )
-  
-  #Column to normalized by
-  if(!is.null(normMethod)){
-    if (tolower(normMethod) %in% c('rc', 'ncells', 'none')){
+  # Column to normalized by
+  if(!is.null(x = normMethod)) {
+    if (tolower(x = normMethod) %in% c('rc', 'ncells', 'none')){
       normBy <- normMethod
     } else{
-      normBy <- object[[normMethod, drop=FALSE]]
+      normBy <- object[[normMethod, drop = FALSE]]
     }
   }
-  
-  #Get chromosome information
-  if(!is.null(chromosome)){
+  # Get chromosome information
+  if(!is.null(x = chromosome)){
     seqlevels(object) <- chromosome
   }
-  
-  availableChr <- names(seqlengths(object))
+  availableChr <- names(x = seqlengths(object))
   chromLengths <- seqlengths(object)
-  chromSizes <- GRanges(seqnames = availableChr, IRanges(start = rep(1, length(availableChr)), end = as.numeric(chromLengths)))
+  chromSizes <- GRanges(
+    seqnames = availableChr,
+    ranges = IRanges(
+      start = rep(1, length(x = availableChr)),
+      end = as.numeric(x = chromLengths)
+      )
+    )
   
   if (verbose) {
-    message("Creation of tiles")
+    message("Creating tiles")
   }
-  
-  #Create tiles for each chromosome, from GenomicRanges
-  tiles <- unlist(slidingWindows(chromSizes, width = tileSize, step = tileSize))
-  
+  # Create tiles for each chromosome, from GenomicRanges
+  tiles <- unlist(
+    x = slidingWindows(x = chromSizes, width = tileSize, step = tileSize)
+  )
   if (verbose) {
-    message("Bigwig files generation at ", outdir)
+    message("Creating bigwig files at ", outdir)
   }
-  
-  #Run the creation of bigwig for each cellgroups
-  
+  # Run the creation of bigwig for each cellgroups
   if (nbrOfWorkers() > 1) { 
     mylapply <- future_lapply 
   } else { 
     mylapply <- ifelse(test = verbose, yes = pblapply, no = lapply) 
   }
-  
-  covFiles <- mylapply(GroupsNames, CreateBWGroup, availableChr, chromLengths, tiles, normBy, tileSize, normMethod, cutoff, outdir)
-  
-  covFiles
-  
+  covFiles <- mylapply(
+    x = GroupsNames,
+    FUN = CreateBWGroup,
+    availableChr,
+    chromLengths,
+    tiles,
+    normBy,
+    tileSize,
+    normMethod,
+    cutoff,
+    outdir
+  )
+  return(covFiles)
 }
 
 # Helper function for ExportGroupBW
@@ -2407,79 +2409,86 @@ ExportGroupBW  <- function(
 #' @importFrom BiocGenerics which
 #' @importFrom S4Vectors match
 #' @importFrom Matrix sparseMatrix rowSums
-CreateBWGroup <- function(groupNamei, availableChr, chromLengths, tiles, normBy, tileSize, normMethod, cutoff, outdir){
-  
-  #Read the fragments file associated to the group
-  fragi <- rtracklayer::import(paste0(outdir, .Platform$file.sep, groupNamei, ".bed"),format = "bed")
-  
-  cellGroupi <- unique(fragi$name)
-  
-  #Open the writting bigwig file
-  covFile <- file.path(outdir, paste0(groupNamei, "-TileSize-",tileSize,"-normMethod-",normMethod,".bw"))
+CreateBWGroup <- function(
+    groupNamei,
+    availableChr,
+    chromLengths,
+    tiles,
+    normBy,
+    tileSize,
+    normMethod,
+    cutoff,
+    outdir
+) {
+  if (!requireNamespace("rtracklayer", quietly = TRUE)) { 
+    message("Please install rtracklayer. http://www.bioconductor.org/packages/rtracklayer/") 
+    return(NULL) 
+  }
+  normMethod <- tolower(x = normMethod)
+  # Read the fragments file associated to the group
+  fragi <- rtracklayer::import(
+    paste0(outdir, .Platform$file.sep, groupNamei, ".bed"), format = "bed"
+  )
+  cellGroupi <- unique(x = fragi$name)
+  # Open the writing bigwig file
+  covFile <- file.path(
+    outdir,
+    paste0(groupNamei, "-TileSize-",tileSize,"-normMethod-",normMethod,".bw")
+  )
   
-  covList <- lapply(seq_along(availableChr), function(k){
-    
+  covList <- lapply(X = seq_along(availableChr), FUN = function(k) {
     fragik <- fragi[seqnames(fragi) == availableChr[k],]
     tilesk <- tiles[BiocGenerics::which(S4Vectors::match(seqnames(tiles), availableChr[k], nomatch = 0) > 0)]
-    
-    if(length(fragik) == 0){
+    if (length(x = fragik) == 0) {
       tilesk$reads <- 0
-      #If fragments
-    }else{
-      
-      #N Tiles
+      # If fragments
+    } else {
+      # N Tiles
       nTiles <- chromLengths[availableChr[k]] / tileSize
-      #Add one tile if there is extra bases
+      # Add one tile if there is extra bases
       if (nTiles%%1 != 0) {
-        nTiles <- trunc(nTiles) + 1
+        nTiles <- trunc(x = nTiles) + 1
       }
-      
-      #Create Sparse Matrix
+      # Create Sparse Matrix
       matchID <- S4Vectors::match(mcols(fragik)$name, cellGroupi)
       
-      #For each tiles of this chromosome, create start tile and end tile row, set the associated counts matching with the fragments
-      mat <- Matrix::sparseMatrix(
-        i = c(trunc(start(fragik) / tileSize), trunc(end(fragik) / tileSize)) + 1,
-        j = as.vector(c(matchID, matchID)),
-        x = rep(1, 2*length(fragik)),
-        dims = c(nTiles, length(cellGroupi)))
+      # For each tiles of this chromosome, create start tile and end tile row,
+      # set the associated counts matching with the fragments
+      mat <- sparseMatrix(
+        i = c(trunc(x = start(x = fragik) / tileSize),
+              trunc(x = end(x = fragik) / tileSize)) + 1,
+        j = as.vector(x = c(matchID, matchID)),
+        x = rep(1, 2*length(x = fragik)),
+        dims = c(nTiles, length(x = cellGroupi))
+      )
       
-      #Max count for a cells in a tile is set to cutoff
-      if(!is.null(cutoff)){
+      # Max count for a cells in a tile is set to cutoff
+      if (!is.null(x = cutoff)){
         mat@x[mat@x > cutoff] <- cutoff
       }
-      
-      #Sums the cells
-      mat <- Matrix::rowSums(mat)
-      
+      # Sums the cells
+      mat <- rowSums(x = mat)
       tilesk$reads <- mat
-      
-      #Normalization
-      if(!is.null(normMethod)){
-        if(tolower(normMethod) == "rc"){
+      # Normalization
+      if (!is.null(x = normMethod)) {
+        if (normMethod == "rc") {
           tilesk$reads <- tilesk$reads * 10^4 / length(fragi$name)
-        }else if(tolower(normMethod) == "ncells"){
+        } else if (normMethod == "ncells") {
           tilesk$reads <- tilesk$reads / length(cellGroupi)
-        }else if(tolower(normMethod) == "none"){
-        }else{
-          if(!is.null(normBy)){
+        } else if (normMethod == "none") {
+        } else {
+          if (!is.null(x = normBy)){
             tilesk$reads <- tilesk$reads * 10^4 / sum(normBy[cellGroupi, 1])
           }
         }
       }
     }
-    
     tilesk <- coverage(tilesk, weight = tilesk$reads)[[availableChr[k]]]
-    
     tilesk
-    
   })
   
   names(covList) <- availableChr
-  
-  covList <- as(covList, "RleList")
-  
+  covList <- as(object = covList, Class = "RleList")
   rtracklayer::export.bw(object = covList, con = covFile)
-  
   return(covFile)
 }
\ No newline at end of file

From e65a74dbe8e489f92b01a2a9c049c67a317c83a0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bastien=20Herv=C3=A9?= <bastienherve61@gmail.com>
Date: Fri, 3 Nov 2023 10:56:37 +0100
Subject: [PATCH 08/34] Update utilities.R

I have an error passing the GroupNames via x
---
 R/utilities.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/utilities.R b/R/utilities.R
index 4854086d..70d6f336 100644
--- a/R/utilities.R
+++ b/R/utilities.R
@@ -2372,7 +2372,7 @@ ExportGroupBW  <- function(
     mylapply <- ifelse(test = verbose, yes = pblapply, no = lapply) 
   }
   covFiles <- mylapply(
-    x = GroupsNames,
+    GroupsNames,
     FUN = CreateBWGroup,
     availableChr,
     chromLengths,
@@ -2491,4 +2491,4 @@ CreateBWGroup <- function(
   covList <- as(object = covList, Class = "RleList")
   rtracklayer::export.bw(object = covList, con = covFile)
   return(covFile)
-}
\ No newline at end of file
+}

From 487bd46e971f4ab4d495f498857455318f7985fc Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Wed, 2 Oct 2024 15:41:41 +0200
Subject: [PATCH 09/34] use GetGroups

---
 R/utilities.R | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/R/utilities.R b/R/utilities.R
index 70d6f336..ad319abb 100644
--- a/R/utilities.R
+++ b/R/utilities.R
@@ -2308,11 +2308,12 @@ ExportGroupBW  <- function(
   }
   assay <- SetIfNull(x = assay, y = DefaultAssay(object = object))
   DefaultAssay(object = object) <- assay
-  group.by <- SetIfNull(x = group.by, y = 'ident')
-  Idents(object = object) <- group.by
-  idents <- SetIfNull(x = idents, y = levels(x = object))
-  GroupsNames <- names(x = table(object[[group.by]])[table(object[[group.by]]) > minCells])
-  GroupsNames <- GroupsNames[GroupsNames %in% idents]
+  obj.groups <- GetGroups(
+    object = object,
+    group.by = group.by,
+    idents = idents
+  )
+  GroupsNames <- names(x = table(obj.groups)[table(obj.groups) > minCells])
   # Check if output files already exist
   lapply(X = GroupsNames, FUN = function(x) {
     fn <- paste0(outdir, .Platform$file.sep, x, ".bed")

From 5271bbc7265049d6c32327e81ad6d4f207dbb4c4 Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Wed, 2 Oct 2024 15:45:43 +0200
Subject: [PATCH 10/34] raise error if outdir is not set

---
 R/utilities.R | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/R/utilities.R b/R/utilities.R
index ad319abb..e9c78f88 100644
--- a/R/utilities.R
+++ b/R/utilities.R
@@ -2298,6 +2298,9 @@ ExportGroupBW  <- function(
     outdir = NULL,
     verbose=TRUE
 ) {
+  if (is.null(outdir)) {
+    stop("Must supply the output directory")
+  }
   # Check if temporary directory exist
   if (!dir.exists(outdir)){
     dir.create(outdir)

From cc56669709d0604b74b7a61be98f88b72a027516 Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Wed, 2 Oct 2024 15:50:15 +0200
Subject: [PATCH 11/34] add an import for nbrOfWorkers

---
 R/utilities.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/utilities.R b/R/utilities.R
index e9c78f88..ac53618d 100644
--- a/R/utilities.R
+++ b/R/utilities.R
@@ -2274,7 +2274,7 @@ SparseSpearmanCor <- function(X, Y = NULL, cov = FALSE) {
 #' @param verbose Display messages
 #'
 #' @importFrom GenomicRanges seqlengths GRanges slidingWindows
-#' @importFrom future plan
+#' @importFrom future plan nbrOfWorkers
 #' @importFrom future.apply future_lapply
 #' @importFrom pbapply pbapply
 #'

From d72e1549c2c98c7c2db4299038a370a4e9f9f973 Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Wed, 2 Oct 2024 17:16:04 +0200
Subject: [PATCH 12/34] set outdir default value to wd

---
 R/utilities.R | 9 +++------
 1 file changed, 3 insertions(+), 6 deletions(-)

diff --git a/R/utilities.R b/R/utilities.R
index ac53618d..8fff1a41 100644
--- a/R/utilities.R
+++ b/R/utilities.R
@@ -2295,19 +2295,16 @@ ExportGroupBW  <- function(
     minCells = 5,
     cutoff = NULL,
     chromosome = NULL,
-    outdir = NULL,
-    verbose=TRUE
+    outdir = getwd(),
+    verbose = TRUE
 ) {
-  if (is.null(outdir)) {
-    stop("Must supply the output directory")
-  }
   # Check if temporary directory exist
   if (!dir.exists(outdir)){
     dir.create(outdir)
   }
   if (!requireNamespace("rtracklayer", quietly = TRUE)) { 
     message("Please install rtracklayer. http://www.bioconductor.org/packages/rtracklayer/") 
-    return(NULL) 
+    return(NULL)
   }
   assay <- SetIfNull(x = assay, y = DefaultAssay(object = object))
   DefaultAssay(object = object) <- assay

From aad0a9b01992ab4b4f94aadce6a54c1f23bdab76 Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Wed, 2 Oct 2024 17:16:53 +0200
Subject: [PATCH 13/34] change help for outdir to match SplitFragments

---
 R/utilities.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/utilities.R b/R/utilities.R
index 8fff1a41..6c23ee34 100644
--- a/R/utilities.R
+++ b/R/utilities.R
@@ -2270,7 +2270,7 @@ SparseSpearmanCor <- function(X, Y = NULL, cov = FALSE) {
 #' @param minCells The minimum of cells in a group to be exported
 #' @param cutoff The maximum number of fragments in a given genomic tile
 #' @param chromosome A chromosomes vector to be exported
-#' @param outdir The output directory for bigwig file
+#' @param outdir Directory to write output files (splitted bed and bigwigs)
 #' @param verbose Display messages
 #'
 #' @importFrom GenomicRanges seqlengths GRanges slidingWindows

From 093074df59e0611547b3a7b651f08938c05d493c Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Wed, 2 Oct 2024 17:17:24 +0200
Subject: [PATCH 14/34] remove unneeded change of DefaultAssay

---
 R/utilities.R | 1 -
 1 file changed, 1 deletion(-)

diff --git a/R/utilities.R b/R/utilities.R
index 6c23ee34..e98c519c 100644
--- a/R/utilities.R
+++ b/R/utilities.R
@@ -2307,7 +2307,6 @@ ExportGroupBW  <- function(
     return(NULL)
   }
   assay <- SetIfNull(x = assay, y = DefaultAssay(object = object))
-  DefaultAssay(object = object) <- assay
   obj.groups <- GetGroups(
     object = object,
     group.by = group.by,

From c6e81e731676d6ac82e5730f3d125a1bd09aa5d6 Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Wed, 2 Oct 2024 17:17:46 +0200
Subject: [PATCH 15/34] raise an error if the object has no Fragments

---
 R/utilities.R | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/R/utilities.R b/R/utilities.R
index e98c519c..86b98cc1 100644
--- a/R/utilities.R
+++ b/R/utilities.R
@@ -2306,6 +2306,9 @@ ExportGroupBW  <- function(
     message("Please install rtracklayer. http://www.bioconductor.org/packages/rtracklayer/") 
     return(NULL)
   }
+  if (length(Fragments(object)) == 0) {
+    stop("This object does not have Fragments, cannot generate bigwig.")
+  }
   assay <- SetIfNull(x = assay, y = DefaultAssay(object = object))
   obj.groups <- GetGroups(
     object = object,

From bfa0d217a3bfa8bef7061a011f451559b46e52dc Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Wed, 2 Oct 2024 20:59:45 +0200
Subject: [PATCH 16/34] add tests

---
 tests/testthat/test-utilities.R | 71 +++++++++++++++++++++++++++++++++
 1 file changed, 71 insertions(+)

diff --git a/tests/testthat/test-utilities.R b/tests/testthat/test-utilities.R
index 45f69377..e0f0f3b1 100644
--- a/tests/testthat/test-utilities.R
+++ b/tests/testthat/test-utilities.R
@@ -67,3 +67,74 @@ test_that("ExtractCell works", {
     object = ExtractCell(x = "chr1\t1\t300\tTGCA\t1"), expected = "TGCA"
   )
 })
+
+test_that("CreateBWGroup works", {
+  outdir <- file.path(tempdir(), "createBW")
+  dir.create(outdir, showWarnings = FALSE)
+  fpath <- system.file("extdata", "fragments.tsv.gz", package="Signac")
+  cells <- colnames(x = atac_small)
+  names(x = cells) <- cells
+  frags <- CreateFragmentObject(
+    path = fpath,
+    cells = cells,
+    verbose = FALSE,
+    validate = FALSE
+  )
+  Fragments(atac_small) <- frags
+  SplitFragments(
+    object = atac_small,
+    assay = "peaks",
+    group.by = "seurat_clusters",
+    outdir = outdir
+  )
+  CreateBWGroup(
+    groupNamei = "0",
+    availableChr = "chr1",
+    chromLengths = c("chr1" = 249250621),
+    tiles = GRanges(seqnames = "chr1", ranges = IRanges(start = 1, end = 249250621)),
+    normBy = NULL,
+    tileSize = 249250621,
+    normMethod = 'RC',
+    cutoff = NULL,
+    outdir = outdir
+  )
+  expect_equal(object = length(list.files(outdir)), expected = 3)
+  expect(file.exists(file.path(outdir, "0-TileSize-249250621-normMethod-rc.bw")), "File does not exist.")
+  bw <- rtracklayer::import.bw(file.path(outdir, "0-TileSize-249250621-normMethod-rc.bw"))
+  expect_equal(object = bw$score, 20000)
+})
+
+test_that("ExportGroupBW works", {
+  outdir <- file.path(tempdir(), "ExportGroupBW")
+  dir.create(outdir, showWarnings = FALSE)
+  fpath <- system.file("extdata", "fragments.tsv.gz", package="Signac")
+  cells <- colnames(x = atac_small)
+  names(x = cells) <- cells
+  frags <- CreateFragmentObject(
+    path = fpath,
+    cells = cells,
+    verbose = FALSE,
+    validate = FALSE
+  )
+  Fragments(atac_small) <- frags
+  ExportGroupBW(
+    object = atac_small,
+    assay = NULL,
+    group.by = NULL,
+    idents = NULL,
+    normMethod = "RC",
+    tileSize = 100,
+    minCells = 5,
+    cutoff = NULL,
+    chromosome = NULL,
+    outdir = outdir,
+    verbose = TRUE
+  )
+  expect_equal(object = length(list.files(outdir)), expected = 4)
+  expect(
+    file.exists(file.path(outdir, "0-TileSize-100-normMethod-rc.bw")),
+    "File does not exist."
+  )
+  bw <- rtracklayer::import.bw(file.path(outdir, "0-TileSize-100-normMethod-rc.bw"))
+  assert_equal(object = length(seqlengths(bw)), 298)
+})
\ No newline at end of file

From f7f667b788bbcbb14a24d8d77fa44f083fdd1df7 Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Wed, 2 Oct 2024 21:17:09 +0200
Subject: [PATCH 17/34] run document

---
 NAMESPACE            |  9 +++++++
 R/utilities.R        |  5 ++--
 man/ExportGroupBW.Rd | 57 ++++++++++++++++++++++++++++++++++++++++++++
 3 files changed, 68 insertions(+), 3 deletions(-)
 create mode 100644 man/ExportGroupBW.Rd

diff --git a/NAMESPACE b/NAMESPACE
index 25899c45..218f91a6 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -117,6 +117,7 @@ export(CreateMotifObject)
 export(DensityScatter)
 export(DepthCor)
 export(DownsampleFeatures)
+export(ExportGroupBW)
 export(ExpressionPlot)
 export(Extend)
 export(FRiP)
@@ -216,6 +217,7 @@ importFrom(BiocGenerics,end)
 importFrom(BiocGenerics,sort)
 importFrom(BiocGenerics,start)
 importFrom(BiocGenerics,strand)
+importFrom(BiocGenerics,which)
 importFrom(BiocGenerics,width)
 importFrom(GenomeInfoDb,"genome<-")
 importFrom(GenomeInfoDb,"isCircular<-")
@@ -235,6 +237,7 @@ importFrom(GenomeInfoDb,seqlevels)
 importFrom(GenomeInfoDb,seqnames)
 importFrom(GenomeInfoDb,sortSeqlevels)
 importFrom(GenomicRanges,GRanges)
+importFrom(GenomicRanges,coverage)
 importFrom(GenomicRanges,disjoin)
 importFrom(GenomicRanges,end)
 importFrom(GenomicRanges,findOverlaps)
@@ -244,6 +247,7 @@ importFrom(GenomicRanges,makeGRangesFromDataFrame)
 importFrom(GenomicRanges,reduce)
 importFrom(GenomicRanges,resize)
 importFrom(GenomicRanges,seqnames)
+importFrom(GenomicRanges,slidingWindows)
 importFrom(GenomicRanges,start)
 importFrom(GenomicRanges,strand)
 importFrom(GenomicRanges,tileGenome)
@@ -290,6 +294,7 @@ importFrom(Rsamtools,scanTabix)
 importFrom(Rsamtools,seqnamesTabix)
 importFrom(S4Vectors,"mcols<-")
 importFrom(S4Vectors,elementNROWS)
+importFrom(S4Vectors,match)
 importFrom(S4Vectors,mcols)
 importFrom(S4Vectors,queryHits)
 importFrom(S4Vectors,split)
@@ -318,6 +323,7 @@ importFrom(dplyr,top_n)
 importFrom(dplyr,ungroup)
 importFrom(fastmatch,fmatch)
 importFrom(future,nbrOfWorkers)
+importFrom(future,plan)
 importFrom(future.apply,future_lapply)
 importFrom(ggplot2,aes)
 importFrom(ggplot2,aes_string)
@@ -381,8 +387,11 @@ importFrom(methods,slotNames)
 importFrom(patchwork,guide_area)
 importFrom(patchwork,plot_layout)
 importFrom(patchwork,wrap_plots)
+importFrom(pbapply,pbapply)
 importFrom(pbapply,pblapply)
 importFrom(rlang,.data)
+importFrom(rtracklayer,export.bw)
+importFrom(rtracklayer,import)
 importFrom(scales,comma)
 importFrom(scales,hue_pal)
 importFrom(stats,approx)
diff --git a/R/utilities.R b/R/utilities.R
index 86b98cc1..102fbdd5 100644
--- a/R/utilities.R
+++ b/R/utilities.R
@@ -2273,12 +2273,11 @@ SparseSpearmanCor <- function(X, Y = NULL, cov = FALSE) {
 #' @param outdir Directory to write output files (splitted bed and bigwigs)
 #' @param verbose Display messages
 #'
-#' @importFrom GenomicRanges seqlengths GRanges slidingWindows
+#' @importFrom GenomicRanges GRanges slidingWindows
 #' @importFrom future plan nbrOfWorkers
 #' @importFrom future.apply future_lapply
 #' @importFrom pbapply pbapply
 #'
-#' @return
 #' @export
 #'
 #' @examples
@@ -2408,7 +2407,7 @@ ExportGroupBW  <- function(
 # @param outdir The output directory for bigwig file
 #
 #' @importFrom rtracklayer import export.bw
-#' @importFrom GenomicRanges seqnames seqlengths GRanges coverage
+#' @importFrom GenomicRanges seqnames GRanges coverage
 #' @importFrom BiocGenerics which
 #' @importFrom S4Vectors match
 #' @importFrom Matrix sparseMatrix rowSums
diff --git a/man/ExportGroupBW.Rd b/man/ExportGroupBW.Rd
new file mode 100644
index 00000000..9a7c684a
--- /dev/null
+++ b/man/ExportGroupBW.Rd
@@ -0,0 +1,57 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/utilities.R
+\name{ExportGroupBW}
+\alias{ExportGroupBW}
+\title{Export bigwig files for groups of cells}
+\usage{
+ExportGroupBW(
+  object,
+  assay = NULL,
+  group.by = NULL,
+  idents = NULL,
+  normMethod = "RC",
+  tileSize = 100,
+  minCells = 5,
+  cutoff = NULL,
+  chromosome = NULL,
+  outdir = getwd(),
+  verbose = TRUE
+)
+}
+\arguments{
+\item{object}{A Seurat object}
+
+\item{assay}{Name of assay to use}
+
+\item{group.by}{The metadata variable used to group the cells}
+
+\item{idents}{Identities to include (defined by group.by parameter)}
+
+\item{normMethod}{Normalization method for the bigwig files. Deafult 'RC'.
+'RC' will divide the number of fragments in a tile by the total number of
+fragments in the group. A scaling factor of 10^4 will be applied. 
+'ncells' will divide the number of fragments in a tile by the number of cell
+in the group. 'none' will apply no normalization method. 
+A vector of values for each cell can also be passed as a metadata column
+name. A scaling factor of 10^4 will be applied}
+
+\item{tileSize}{The size of the tiles in the bigwig file}
+
+\item{minCells}{The minimum of cells in a group to be exported}
+
+\item{cutoff}{The maximum number of fragments in a given genomic tile}
+
+\item{chromosome}{A chromosomes vector to be exported}
+
+\item{outdir}{Directory to write output files (splitted bed and bigwigs)}
+
+\item{verbose}{Display messages}
+}
+\description{
+Export bigwig files for groups of cells
+}
+\examples{
+\dontrun{
+ExportGroupBW(object, assay = "peaks")
+}
+}

From b849dab48bf3d547d644adc20199b25f396c16a9 Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Wed, 2 Oct 2024 21:24:50 +0200
Subject: [PATCH 18/34] Add rtracklayer to the Imports

---
 DESCRIPTION | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 55b27307..15a334fe 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -51,7 +51,8 @@ Imports:
     Rcpp,
     grid,
     tidyselect,
-    vctrs
+    vctrs,
+    rtracklayer
 Collate: 
     'RcppExports.R'
     'data.R'
@@ -88,7 +89,6 @@ Suggests:
     BSgenome,
     shiny,
     miniUI,
-    rtracklayer,
     biovizBase,
     Biostrings,
     lsa,

From 74f5fae1646fc1661ca26d43c945ec029561245b Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Wed, 2 Oct 2024 21:34:49 +0200
Subject: [PATCH 19/34] remove unneeded check for rtracklayer

---
 R/utilities.R | 8 --------
 1 file changed, 8 deletions(-)

diff --git a/R/utilities.R b/R/utilities.R
index 102fbdd5..c9cb86a4 100644
--- a/R/utilities.R
+++ b/R/utilities.R
@@ -2301,10 +2301,6 @@ ExportGroupBW  <- function(
   if (!dir.exists(outdir)){
     dir.create(outdir)
   }
-  if (!requireNamespace("rtracklayer", quietly = TRUE)) { 
-    message("Please install rtracklayer. http://www.bioconductor.org/packages/rtracklayer/") 
-    return(NULL)
-  }
   if (length(Fragments(object)) == 0) {
     stop("This object does not have Fragments, cannot generate bigwig.")
   }
@@ -2422,10 +2418,6 @@ CreateBWGroup <- function(
     cutoff,
     outdir
 ) {
-  if (!requireNamespace("rtracklayer", quietly = TRUE)) { 
-    message("Please install rtracklayer. http://www.bioconductor.org/packages/rtracklayer/") 
-    return(NULL) 
-  }
   normMethod <- tolower(x = normMethod)
   # Read the fragments file associated to the group
   fragi <- rtracklayer::import(

From c555f6cca5b529809f08b3f342fe66b224104cc9 Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Wed, 2 Oct 2024 21:34:56 +0200
Subject: [PATCH 20/34] fix assert to expect

---
 tests/testthat/test-utilities.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/testthat/test-utilities.R b/tests/testthat/test-utilities.R
index e0f0f3b1..8a1403a9 100644
--- a/tests/testthat/test-utilities.R
+++ b/tests/testthat/test-utilities.R
@@ -136,5 +136,5 @@ test_that("ExportGroupBW works", {
     "File does not exist."
   )
   bw <- rtracklayer::import.bw(file.path(outdir, "0-TileSize-100-normMethod-rc.bw"))
-  assert_equal(object = length(seqlengths(bw)), 298)
+  expect_equal(object = length(seqlengths(bw)), 298)
 })
\ No newline at end of file

From 0109f1dc86334dfeb0c1ccd840227de7ff2792dc Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Wed, 2 Oct 2024 23:00:11 +0200
Subject: [PATCH 21/34] use more controled tests for CreateBWGroup

---
 tests/testthat/test-utilities.R | 60 ++++++++++++++++++++++++---------
 1 file changed, 44 insertions(+), 16 deletions(-)

diff --git a/tests/testthat/test-utilities.R b/tests/testthat/test-utilities.R
index 8a1403a9..23d7390b 100644
--- a/tests/testthat/test-utilities.R
+++ b/tests/testthat/test-utilities.R
@@ -68,24 +68,20 @@ test_that("ExtractCell works", {
   )
 })
 
-test_that("CreateBWGroup works", {
+test_that("CreateBWGroup works with single tile", {
   outdir <- file.path(tempdir(), "createBW")
   dir.create(outdir, showWarnings = FALSE)
-  fpath <- system.file("extdata", "fragments.tsv.gz", package="Signac")
-  cells <- colnames(x = atac_small)
-  names(x = cells) <- cells
-  frags <- CreateFragmentObject(
-    path = fpath,
-    cells = cells,
-    verbose = FALSE,
-    validate = FALSE
+  fake.bed.data <- data.frame(
+    seqnames = rep("chr1", 5),
+    start = c(0, 10, 100, 110, 300),
+    end = c(100, 150, 200, 250, 500),
+    cell_name = rep("fake_cell", 5),
+    nb = 1:5
   )
-  Fragments(atac_small) <- frags
-  SplitFragments(
-    object = atac_small,
-    assay = "peaks",
-    group.by = "seurat_clusters",
-    outdir = outdir
+  write.table(
+    fake.bed.data, file.path(outdir, "0.bed"),
+    col.names = FALSE, quote = FALSE, sep = "\t",
+    row.names = FALSE
   )
   CreateBWGroup(
     groupNamei = "0",
@@ -98,12 +94,44 @@ test_that("CreateBWGroup works", {
     cutoff = NULL,
     outdir = outdir
   )
-  expect_equal(object = length(list.files(outdir)), expected = 3)
+  expect_equal(object = length(list.files(outdir)), expected = 2)
   expect(file.exists(file.path(outdir, "0-TileSize-249250621-normMethod-rc.bw")), "File does not exist.")
   bw <- rtracklayer::import.bw(file.path(outdir, "0-TileSize-249250621-normMethod-rc.bw"))
   expect_equal(object = bw$score, 20000)
 })
 
+test_that("CreateBWGroup works with 100bp tile", {
+  outdir <- file.path(tempdir(), "createBW2")
+  dir.create(outdir, showWarnings = FALSE)
+  fake.bed.data <- data.frame(
+    seqnames = rep("chr1", 5),
+    start = c(0, 10, 100, 110, 300),
+    end = c(100, 150, 200, 250, 500),
+    cell_name = rep("fake_cell", 5),
+    nb = 1:5
+  )
+  write.table(
+    fake.bed.data, file.path(outdir, "0.bed"),
+    col.names = FALSE, quote = FALSE, sep = "\t",
+    row.names = FALSE
+  )
+  CreateBWGroup(
+    groupNamei = "0",
+    availableChr = "chr1",
+    chromLengths = c("chr1" = 249250621),
+    tiles = GRanges(seqnames = "chr1", ranges = IRanges(start = seq(1, 249250621, 100), end = c(seq(100, 249250621, 100), 249250621))),
+    normBy = NULL,
+    tileSize = 100,
+    normMethod = "RC",
+    cutoff = NULL,
+    outdir = outdir
+  )
+  expect_equal(object = length(list.files(outdir)), expected = 2)
+  expect(file.exists(file.path(outdir, "0-TileSize-100-normMethod-rc.bw")), "File does not exist.")
+  bw <- rtracklayer::import.bw(file.path(outdir, "0-TileSize-100-normMethod-rc.bw"))
+  expect_equal(object = bw$score, c(4000, 8000, 4000, 2000, 0, 2000, 0))
+})
+
 test_that("ExportGroupBW works", {
   outdir <- file.path(tempdir(), "ExportGroupBW")
   dir.create(outdir, showWarnings = FALSE)

From 3b1cf35076eb3e3118e69a8bfb67043fd35f37b2 Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Wed, 2 Oct 2024 23:01:28 +0200
Subject: [PATCH 22/34] remove spaces in empty lines

---
 R/utilities.R | 66 +++++++++++++++++++++++++--------------------------
 1 file changed, 33 insertions(+), 33 deletions(-)

diff --git a/R/utilities.R b/R/utilities.R
index c9cb86a4..b532df50 100644
--- a/R/utilities.R
+++ b/R/utilities.R
@@ -39,13 +39,13 @@ AddChromatinModule <- function(
   if (!inherits(x = object[[assay]], what = "ChromatinAssay")) {
     stop("The requested assay is not a ChromatinAssay.")
   }
-  
+
   # first find index of each feature
   feat.idx <- sapply(X = features, FUN = fmatch, rownames(x = object[[assay]]))
   j <- sapply(X = seq_along(along.with = features), FUN = function(x) {
     rep(x = x, length(x = features[[x]]))
   })
-  
+
   # construct sparse matrix with features
   mat <- sparseMatrix(
     i = unlist(x = feat.idx, use.names = FALSE),
@@ -55,7 +55,7 @@ AddChromatinModule <- function(
   )
   rownames(x = mat) <- rownames(x = object[[assay]])
   colnames(x = mat) <- names(x = features)
-  
+
   # run chromVAR
   cv <- RunChromVAR(
     object = object[[assay]],
@@ -64,7 +64,7 @@ AddChromatinModule <- function(
     verbose = verbose,
     ...
   )
-  
+
   # add module scores to metadata
   chromvar.data <- GetAssayData(object = cv, slot = "data")
   object <- AddMetaData(
@@ -334,7 +334,7 @@ GeneActivity <- function(
       stop("No genes remaining after filtering for requested biotypes")
     }
   }
-  
+
   # filter genes if provided
   if (!is.null(x = features)) {
     transcripts <- transcripts[transcripts$gene_name %in% features]
@@ -349,14 +349,14 @@ GeneActivity <- function(
       stop("No genes remaining after filtering for max.width")
     }
   }
-  
+
   # extend to include promoters
   transcripts <- Extend(
     x = transcripts,
     upstream = extend.upstream,
     downstream = extend.downstream
   )
-  
+
   # quantify
   frags <- Fragments(object = object[[assay]])
   if (length(x = frags) == 0) {
@@ -375,7 +375,7 @@ GeneActivity <- function(
   names(x = gene.key) <- GRangesToString(grange = transcripts)
   rownames(x = counts) <- as.vector(x = gene.key[rownames(x = counts)])
   counts <- counts[rownames(x = counts) != "", ]
-  
+
   return(counts)
 }
 
@@ -409,7 +409,7 @@ GetGRangesFromEnsDb <- function(
   if (standard.chromosomes) {
     whole.genome <- keepStandardChromosomes(whole.genome, pruning.mode = "coarse")
   }
-  
+
   # extract genes from each chromosome
   my_lapply <- ifelse(test = verbose, yes = pblapply, no = lapply)
   tx <- my_lapply(X = seq_along(whole.genome), FUN = function(x){
@@ -418,7 +418,7 @@ GetGRangesFromEnsDb <- function(
       which = whole.genome[x],
       columns = c("tx_id", "gene_name", "gene_id", "gene_biotype")))
   })
-  
+
   # combine
   tx <- do.call(what = c, args = tx)
   tx <- tx[tx$gene_biotype %in% biotypes]
@@ -1307,7 +1307,7 @@ GetReadsInRegion <- function(
 ) {
   file.to.object <- names(x = cellmap)
   names(x = file.to.object) <- cellmap
-  
+
   if (verbose) {
     message("Extracting reads in requested region")
   }
@@ -1679,7 +1679,7 @@ CreateRegionPileupMatrix <- function(
   on_plus <- strand(x = regions) == "+" | strand(x = regions) == "*"
   plus.strand <- regions[on_plus, ]
   minus.strand <- regions[!on_plus, ]
-  
+
   # get cut matrices for each strand
   if (verbose) {
     message("Finding + strand cut sites")
@@ -1701,7 +1701,7 @@ CreateRegionPileupMatrix <- function(
     cells = cells,
     verbose = FALSE
   )
-  
+
   # reverse minus strand and add together
   if (is.null(x = cut.matrix.plus)) {
     full.matrix <- cut.matrix.minus[, rev(x = colnames(x = cut.matrix.minus))]
@@ -1755,13 +1755,13 @@ ApplyMatrixByGroup <- function(
   }
   ngroup <- length(x = all.groups)
   npos <- ncol(x = mat)
-  
+
   group <- unlist(
     x = lapply(X = all.groups, FUN = function(x) rep(x, npos))
   )
   position <- rep(x = as.numeric(x = colnames(x = mat)), ngroup)
   count <- vector(mode = "numeric", length = npos * ngroup)
-  
+
   for (i in seq_along(along.with = all.groups)) {
     grp <- all.groups[[i]]
     if (is.na(x = grp)) {
@@ -1776,13 +1776,13 @@ ApplyMatrixByGroup <- function(
     }
     count[((i - 1) * npos + 1):((i * npos))] <- totals
   }
-  
+
   # construct dataframe
   coverages <- data.frame(
     "group" = group, "position" = position, "count" = count,
     stringsAsFactors = FALSE
   )
-  
+
   if (normalize) {
     scale.factor <- SetIfNull(
       x = scale.factor, y = median(x = group.scale.factors)
@@ -1911,12 +1911,12 @@ IsMatrixEmpty <- function(x) {
 # information
 GetRowsToMerge <- function(assay.list, all.ranges, reduced.ranges) {
   revmap <- as.vector(x = reduced.ranges$revmap)
-  
+
   # get indices of ranges that changed
   revmap.lengths <- sapply(X = revmap, FUN = length)
   changed.ranges <- which(x = revmap.lengths > 1)
   grange.string <- GRangesToString(grange = reduced.ranges[changed.ranges])
-  
+
   # preallocate
   offsets <- list()
   results <- list()
@@ -1935,7 +1935,7 @@ GetRowsToMerge <- function(assay.list, all.ranges, reduced.ranges) {
     results[['matrix']][[i]] <- matrix.indices
     results[['grange']][[i]] <- granges
   }
-  
+
   # find sets of ranges for each dataset
   counter <- vector(mode = "numeric", length = length(x = assay.list))
   for (x in seq_along(along.with = changed.ranges)) {
@@ -1992,15 +1992,15 @@ MergeOverlappingRows <- function(
       )
       return(merge.counts)
     }
-    
+
     # transpose for faster access since matrix is column major
     counts <- t(x = counts)
-    
+
     # get rows to merge
     mrows <- mergeinfo$matrix[[i]]
     new.rownames <- mergeinfo$grange[[i]]
     nrep <- rle(x = new.rownames)
-    
+
     # allocate
     todelete <- c()
     newmat <- vector(
@@ -2058,13 +2058,13 @@ MergeOverlappingRows <- function(
     to.rename.names <- to.rename.names[1:idx.counter]
     newmat <- newmat[1:(y - 1)]
     newmat.names <- newmat.names[1:(y - 1)]
-    
+
     # transpose back
     counts <- t(x = counts)
-    
+
     # rename matrix rows that weren't merged
     rownames(counts)[to.rename.idx] <- to.rename.names
-    
+
     if (y == 1) {
       # no rows were merged, can return counts
       merge.counts[[i]] <- counts
@@ -2084,12 +2084,12 @@ MergeOverlappingRows <- function(
       merged.mat <- Reduce(f = rbind, x = newmat)
       rownames(merged.mat) <- newmat.names
       merged.mat <- as(object = merged.mat, Class = "CsparseMatrix")
-      
+
       # remove rows from count matrix that were merged
       mat.rows <- seq_len(length.out = nrow(x = counts))
       tokeep <- setdiff(mat.rows, todelete)
       counts <- counts[tokeep, ]
-      
+
       # add new merged rows to counts
       counts <- rbind(counts, merged.mat)
       merge.counts[[i]] <- counts
@@ -2352,7 +2352,7 @@ ExportGroupBW  <- function(
       end = as.numeric(x = chromLengths)
       )
     )
-  
+
   if (verbose) {
     message("Creating tiles")
   }
@@ -2429,7 +2429,7 @@ CreateBWGroup <- function(
     outdir,
     paste0(groupNamei, "-TileSize-",tileSize,"-normMethod-",normMethod,".bw")
   )
-  
+
   covList <- lapply(X = seq_along(availableChr), FUN = function(k) {
     fragik <- fragi[seqnames(fragi) == availableChr[k],]
     tilesk <- tiles[BiocGenerics::which(S4Vectors::match(seqnames(tiles), availableChr[k], nomatch = 0) > 0)]
@@ -2445,7 +2445,7 @@ CreateBWGroup <- function(
       }
       # Create Sparse Matrix
       matchID <- S4Vectors::match(mcols(fragik)$name, cellGroupi)
-      
+
       # For each tiles of this chromosome, create start tile and end tile row,
       # set the associated counts matching with the fragments
       mat <- sparseMatrix(
@@ -2455,7 +2455,7 @@ CreateBWGroup <- function(
         x = rep(1, 2*length(x = fragik)),
         dims = c(nTiles, length(x = cellGroupi))
       )
-      
+
       # Max count for a cells in a tile is set to cutoff
       if (!is.null(x = cutoff)){
         mat@x[mat@x > cutoff] <- cutoff
@@ -2480,7 +2480,7 @@ CreateBWGroup <- function(
     tilesk <- coverage(tilesk, weight = tilesk$reads)[[availableChr[k]]]
     tilesk
   })
-  
+
   names(covList) <- availableChr
   covList <- as(object = covList, Class = "RleList")
   rtracklayer::export.bw(object = covList, con = covFile)

From 3f4ba003f445c98e4fcfdc99c0595a081796a4b4 Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Wed, 2 Oct 2024 23:06:24 +0200
Subject: [PATCH 23/34] restore 2 space indentation for params

---
 R/utilities.R | 294 +++++++++++++++++++++++++-------------------------
 1 file changed, 147 insertions(+), 147 deletions(-)

diff --git a/R/utilities.R b/R/utilities.R
index b532df50..cd741aa3 100644
--- a/R/utilities.R
+++ b/R/utilities.R
@@ -28,12 +28,12 @@ NULL
 #' @export
 #' @concept utilities
 AddChromatinModule <- function(
-    object,
-    features,
-    genome,
-    assay = NULL,
-    verbose = TRUE,
-    ...
+  object,
+  features,
+  genome,
+  assay = NULL,
+  verbose = TRUE,
+  ...
 ) {
   assay <- SetIfNull(x = assay, y = DefaultAssay(object = object))
   if (!inherits(x = object[[assay]], what = "ChromatinAssay")) {
@@ -92,10 +92,10 @@ globalVariables(names = c("group", "readcount"), package = "Signac")
 #' @examples
 #' AverageCounts(atac_small)
 AverageCounts <- function(
-    object,
-    assay = NULL,
-    group.by = NULL,
-    verbose = TRUE
+  object,
+  assay = NULL,
+  group.by = NULL,
+  verbose = TRUE
 ) {
   assay <- SetIfNull(x = assay, y = DefaultAssay(object = object))
   if (is.null(x = group.by)) {
@@ -135,11 +135,11 @@ AverageCounts <- function(
 #' @importFrom Matrix rowSums
 #' @return Returns a vector of peak names
 AccessiblePeaks <- function(
-    object,
-    assay = NULL,
-    idents = NULL,
-    cells = NULL,
-    min.cells = 10
+  object,
+  assay = NULL,
+  idents = NULL,
+  cells = NULL,
+  min.cells = 10
 ) {
   assay <- SetIfNull(x = assay, y = DefaultAssay(object = object))
   cells <- SetIfNull(x = cells, y = WhichCells(object, idents = idents))
@@ -165,8 +165,8 @@ AccessiblePeaks <- function(
 #' @examples
 #' CellsPerGroup(atac_small)
 CellsPerGroup <- function(
-    object,
-    group.by = NULL
+  object,
+  group.by = NULL
 ) {
   if (is.null(x = group.by)) {
     cellgroups <- Idents(object = object)
@@ -207,10 +207,10 @@ CellsPerGroup <- function(
 #' )
 #' }
 ClosestFeature <- function(
-    object,
-    regions,
-    annotation = NULL,
-    ...
+  object,
+  regions,
+  annotation = NULL,
+  ...
 ) {
   if (!is(object = regions, class2 = 'GRanges')) {
     regions <- StringToGRanges(regions = regions, ...)
@@ -290,16 +290,16 @@ ClosestFeature <- function(
 #' Fragments(atac_small) <- fragments
 #' GeneActivity(atac_small)
 GeneActivity <- function(
-    object,
-    assay = NULL,
-    features = NULL,
-    extend.upstream = 2000,
-    extend.downstream = 0,
-    biotypes = "protein_coding",
-    max.width = 500000,
-    process_n = 2000,
-    gene.id = FALSE,
-    verbose = TRUE
+  object,
+  assay = NULL,
+  features = NULL,
+  extend.upstream = 2000,
+  extend.downstream = 0,
+  biotypes = "protein_coding",
+  max.width = 500000,
+  process_n = 2000,
+  gene.id = FALSE,
+  verbose = TRUE
 ) {
   if (!is.null(x = features)) {
     if (length(x = features) == 0) {
@@ -395,10 +395,10 @@ GeneActivity <- function(
 #' @concept utilities
 #' @export
 GetGRangesFromEnsDb <- function(
-    ensdb,
-    standard.chromosomes = TRUE,
-    biotypes = c("protein_coding", "lincRNA", "rRNA", "processed_transcript"),
-    verbose = TRUE
+  ensdb,
+  standard.chromosomes = TRUE,
+  biotypes = c("protein_coding", "lincRNA", "rRNA", "processed_transcript"),
+  verbose = TRUE
 ) {
   if (!requireNamespace("biovizBase", quietly = TRUE)) {
     stop("Please install biovizBase\n",
@@ -486,12 +486,12 @@ GetTSSPositions <- function(ranges, biotypes = "protein_coding") {
 #'   assay.2 = 'bins'
 #' )
 GetIntersectingFeatures <- function(
-    object.1,
-    object.2,
-    assay.1 = NULL,
-    assay.2 = NULL,
-    distance = 0,
-    verbose = TRUE
+  object.1,
+  object.2,
+  assay.1 = NULL,
+  assay.2 = NULL,
+  distance = 0,
+  verbose = TRUE
 ) {
   assay.1 <- SetIfNull(x = assay.1, y = DefaultAssay(object = object.1))
   assay.2 <- SetIfNull(x = assay.2, y = DefaultAssay(object = object.2))
@@ -591,10 +591,10 @@ GRangesToString <- function(grange, sep = c("-", "-")) {
 #' @examples
 #' Extend(x = blacklist_hg19, upstream = 100, downstream = 100)
 Extend <- function(
-    x,
-    upstream = 0,
-    downstream = 0,
-    from.midpoint = FALSE
+  x,
+  upstream = 0,
+  downstream = 0,
+  from.midpoint = FALSE
 ) {
   if (any(strand(x = x) == "*")) {
     warning("'*' ranges were treated as '+'")
@@ -683,10 +683,10 @@ GetCellsInRegion <- function(tabix, region, cells = NULL) {
 #' )
 #' }
 CountsInRegion <- function(
-    object,
-    assay,
-    regions,
-    ...
+  object,
+  assay,
+  regions,
+  ...
 ) {
   if (!is(object = object[[assay]], class2 = "ChromatinAssay")) {
     stop("Must supply a ChromatinAssay")
@@ -724,10 +724,10 @@ CountsInRegion <- function(
 #' )
 #' }
 FractionCountsInRegion <- function(
-    object,
-    regions,
-    assay = NULL,
-    ...
+  object,
+  regions,
+  assay = NULL,
+  ...
 ) {
   assay <- SetIfNull(x = assay, y = DefaultAssay(object = object))
   reads.in.region <- CountsInRegion(
@@ -772,12 +772,12 @@ FractionCountsInRegion <- function(
 #' "chr1-762106-763359","chr1-779589-780271")
 #' IntersectMatrix(matrix = counts, regions = blacklist_hg19)
 IntersectMatrix <- function(
-    matrix,
-    regions,
-    invert = FALSE,
-    sep = c("-", "-"),
-    verbose = TRUE,
-    ...
+  matrix,
+  regions,
+  invert = FALSE,
+  sep = c("-", "-"),
+  verbose = TRUE,
+  ...
 ) {
   if (is(object = regions, class2 = "character")) {
     regions <- StringToGRanges(regions = regions, sep = sep)
@@ -880,12 +880,12 @@ LookupGeneCoords <- function(object, gene, assay = NULL) {
 #'   n = 10
 #' )
 MatchRegionStats <- function(
-    meta.feature,
-    query.feature,
-    features.match = c("GC.percent"),
-    n = 10000,
-    verbose = TRUE,
-    ...
+  meta.feature,
+  query.feature,
+  features.match = c("GC.percent"),
+  n = 10000,
+  verbose = TRUE,
+  ...
 ) {
   if (!inherits(x = meta.feature, what = 'data.frame')) {
     stop("meta.feature should be a data.frame")
@@ -997,11 +997,11 @@ UnifyPeaks <- function(object.list, mode = "reduce") {
 #' @examples
 #' SubsetMatrix(mat = volcano)
 SubsetMatrix <- function(
-    mat,
-    min.rows = 1,
-    min.cols = 1,
-    max.row.val = 10,
-    max.col.val = NULL
+  mat,
+  min.rows = 1,
+  min.cols = 1,
+  max.row.val = 10,
+  max.col.val = NULL
 ) {
   rowcount <- rowSums(mat > 0)
   colcount <- colSums(mat > 0)
@@ -1053,10 +1053,10 @@ AddMissingCells <- function(x, cells) {
 #' @importFrom SeuratObject DefaultAssay GetAssayData
 #' @importFrom Matrix Diagonal tcrossprod rowSums
 AverageCountMatrix <- function(
-    object,
-    assay = NULL,
-    group.by = NULL,
-    idents = NULL
+  object,
+  assay = NULL,
+  group.by = NULL,
+  idents = NULL
 ) {
   assay = SetIfNull(x = assay, y = DefaultAssay(object = object))
   countmatrix <- GetAssayData(object = object[[assay]], slot = "counts")
@@ -1242,12 +1242,12 @@ ExtractFragments <- function(fragments, n = NULL, verbose = TRUE) {
 # convert region argument to genomic coordinates
 # region can be a string, name of a gene, or GRanges object
 FindRegion <- function(
-    object,
-    region,
-    sep = c("-", "-"),
-    assay = NULL,
-    extend.upstream = 0,
-    extend.downstream = 0
+  object,
+  region,
+  sep = c("-", "-"),
+  assay = NULL,
+  extend.upstream = 0,
+  extend.downstream = 0
 ) {
   if (!is(object = region, class2 = "GRanges")) {
     # first try to convert to coordinates, if not lookup gene
@@ -1298,12 +1298,12 @@ FindRegion <- function(
 #
 # @return Returns a data frame
 GetReadsInRegion <- function(
-    cellmap,
-    region,
-    tabix.file,
-    cells = NULL,
-    verbose = TRUE,
-    ...
+  cellmap,
+  region,
+  tabix.file,
+  cells = NULL,
+  verbose = TRUE,
+  ...
 ) {
   file.to.object <- names(x = cellmap)
   names(x = file.to.object) <- cellmap
@@ -1362,9 +1362,9 @@ GetReadsInRegion <- function(
 # @return Returns a named vector
 #' @importFrom SeuratObject Idents
 GetGroups <- function(
-    object,
-    group.by,
-    idents
+  object,
+  group.by,
+  idents
 ) {
   if (is.null(x = group.by)) {
     obj.groups <- Idents(object = object)
@@ -1414,11 +1414,11 @@ MergeMatrixParts <- function(mat.list, new.rownames) {
 #' @importFrom Rsamtools TabixFile
 #' @importFrom GenomeInfoDb keepSeqlevels
 MultiGetReadsInRegion <- function(
-    object,
-    region,
-    fragment.list = NULL,
-    assay = NULL,
-    ...
+  object,
+  region,
+  fragment.list = NULL,
+  assay = NULL,
+  ...
 ) {
   if (inherits(x = object, what = "Seurat")) {
     # pull the assay
@@ -1471,11 +1471,11 @@ MultiGetReadsInRegion <- function(
 #' @importMethodsFrom GenomicRanges width start end
 # @return Returns a sparse matrix
 SingleFileCutMatrix <- function(
-    cellmap,
-    region,
-    cells = NULL,
-    tabix.file,
-    verbose = TRUE
+  cellmap,
+  region,
+  cells = NULL,
+  tabix.file,
+  verbose = TRUE
 ) {
   # if multiple regions supplied, must be the same width
   cells <- SetIfNull(x = cells, y = names(x = cellmap))
@@ -1541,12 +1541,12 @@ SingleFileCutMatrix <- function(
 #' @importFrom Rsamtools TabixFile seqnamesTabix
 #' @importFrom GenomeInfoDb keepSeqlevels
 CutMatrix <- function(
-    object,
-    region,
-    group.by = NULL,
-    assay = NULL,
-    cells = NULL,
-    verbose = TRUE
+  object,
+  region,
+  group.by = NULL,
+  assay = NULL,
+  cells = NULL,
+  verbose = TRUE
 ) {
   # run SingleFileCutMatrix for each fragment file and combine results
   assay <- SetIfNull(x = assay, y = DefaultAssay(object = object))
@@ -1603,13 +1603,13 @@ CutMatrix <- function(
 #' @importFrom SeuratObject DefaultAssay
 #' @importFrom GenomeInfoDb keepSeqlevels
 MultiRegionCutMatrix <- function(
-    object,
-    regions,
-    group.by = NULL,
-    fragments = NULL,
-    assay = NULL,
-    cells = NULL,
-    verbose = FALSE
+  object,
+  regions,
+  group.by = NULL,
+  fragments = NULL,
+  assay = NULL,
+  cells = NULL,
+  verbose = FALSE
 ) {
   if (inherits(x = object, what = "Seurat")) {
     assay <- SetIfNull(x = assay, y = DefaultAssay(object = object))
@@ -1666,11 +1666,11 @@ MultiRegionCutMatrix <- function(
 # @param verbose Display messages
 #' @importMethodsFrom GenomicRanges strand
 CreateRegionPileupMatrix <- function(
-    object,
-    regions,
-    assay = NULL,
-    cells = NULL,
-    verbose = TRUE
+  object,
+  regions,
+  assay = NULL,
+  cells = NULL,
+  verbose = TRUE
 ) {
   if (length(x = regions) == 0) {
     stop("No regions supplied")
@@ -1737,12 +1737,12 @@ CreateRegionPileupMatrix <- function(
 # @param scale.factor Scaling factor to use. If NULL (default), will use the
 # median normalization factor for all the groups.
 ApplyMatrixByGroup <- function(
-    mat,
-    groups,
-    fun,
-    normalize = TRUE,
-    group.scale.factors = NULL,
-    scale.factor = NULL
+  mat,
+  groups,
+  fun,
+  normalize = TRUE,
+  group.scale.factors = NULL,
+  scale.factor = NULL
 ) {
   if (normalize) {
     if (is.null(x = group.scale.factors) | is.null(x = scale.factor)) {
@@ -1971,10 +1971,10 @@ GetRowsToMerge <- function(assay.list, all.ranges, reduced.ranges) {
 #' @importFrom Matrix rowSums
 #' @importMethodsFrom Matrix t
 MergeOverlappingRows <- function(
-    mergeinfo,
-    assay.list,
-    slot = "counts",
-    verbose = TRUE
+  mergeinfo,
+  assay.list,
+  slot = "counts",
+  verbose = TRUE
 ) {
   merge.counts <- list()
   for (i in seq_along(along.with = assay.list)) {
@@ -2285,17 +2285,17 @@ SparseSpearmanCor <- function(X, Y = NULL, cov = FALSE) {
 #' ExportGroupBW(object, assay = "peaks")
 #' }
 ExportGroupBW  <- function(
-    object,
-    assay = NULL,
-    group.by = NULL,
-    idents = NULL,
-    normMethod = "RC",
-    tileSize = 100,
-    minCells = 5,
-    cutoff = NULL,
-    chromosome = NULL,
-    outdir = getwd(),
-    verbose = TRUE
+  object,
+  assay = NULL,
+  group.by = NULL,
+  idents = NULL,
+  normMethod = "RC",
+  tileSize = 100,
+  minCells = 5,
+  cutoff = NULL,
+  chromosome = NULL,
+  outdir = getwd(),
+  verbose = TRUE
 ) {
   # Check if temporary directory exist
   if (!dir.exists(outdir)){
@@ -2408,15 +2408,15 @@ ExportGroupBW  <- function(
 #' @importFrom S4Vectors match
 #' @importFrom Matrix sparseMatrix rowSums
 CreateBWGroup <- function(
-    groupNamei,
-    availableChr,
-    chromLengths,
-    tiles,
-    normBy,
-    tileSize,
-    normMethod,
-    cutoff,
-    outdir
+  groupNamei,
+  availableChr,
+  chromLengths,
+  tiles,
+  normBy,
+  tileSize,
+  normMethod,
+  cutoff,
+  outdir
 ) {
   normMethod <- tolower(x = normMethod)
   # Read the fragments file associated to the group

From 09203f8dfe69bd42d34926b13d842e5f912904c4 Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Thu, 3 Oct 2024 06:56:22 +0200
Subject: [PATCH 24/34] change bin assignment

---
 R/utilities.R | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/R/utilities.R b/R/utilities.R
index cd741aa3..25979a4f 100644
--- a/R/utilities.R
+++ b/R/utilities.R
@@ -2421,7 +2421,8 @@ CreateBWGroup <- function(
   normMethod <- tolower(x = normMethod)
   # Read the fragments file associated to the group
   fragi <- rtracklayer::import(
-    paste0(outdir, .Platform$file.sep, groupNamei, ".bed"), format = "bed"
+    paste0(outdir, .Platform$file.sep, groupNamei, ".bed"),
+    format = "bed"
   )
   cellGroupi <- unique(x = fragi$name)
   # Open the writing bigwig file
@@ -2448,9 +2449,11 @@ CreateBWGroup <- function(
 
       # For each tiles of this chromosome, create start tile and end tile row,
       # set the associated counts matching with the fragments
+      # This changes compared to ArchR version 1.0.2
+      # See https://github.com/GreenleafLab/ArchR/issues/2214
       mat <- sparseMatrix(
-        i = c(trunc(x = start(x = fragik) / tileSize),
-              trunc(x = end(x = fragik) / tileSize)) + 1,
+        i = c(trunc(x = (start(x = fragik) - 1) / tileSize),
+              trunc(x = (end(x = fragik) - 1) / tileSize)) + 1,
         j = as.vector(x = c(matchID, matchID)),
         x = rep(1, 2*length(x = fragik)),
         dims = c(nTiles, length(x = cellGroupi))

From 2a1d612bef828eb2d446354b32814756c2d0085a Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Thu, 3 Oct 2024 07:01:25 +0200
Subject: [PATCH 25/34] add test with fragment end matching chromosome length

---
 tests/testthat/test-utilities.R | 32 ++++++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)

diff --git a/tests/testthat/test-utilities.R b/tests/testthat/test-utilities.R
index 23d7390b..6b8e8d7d 100644
--- a/tests/testthat/test-utilities.R
+++ b/tests/testthat/test-utilities.R
@@ -132,6 +132,38 @@ test_that("CreateBWGroup works with 100bp tile", {
   expect_equal(object = bw$score, c(4000, 8000, 4000, 2000, 0, 2000, 0))
 })
 
+test_that("CreateBWGroup works with seqlength equal to final pos", {
+  outdir <- file.path(tempdir(), "createBW2")
+  dir.create(outdir, showWarnings = FALSE)
+  fake.bed.data <- data.frame(
+    seqnames = rep("chr1", 5),
+    start = c(0, 10, 100, 110, 300),
+    end = c(100, 150, 200, 250, 500),
+    cell_name = rep("fake_cell", 5),
+    nb = 1:5
+  )
+  write.table(
+    fake.bed.data, file.path(outdir, "0.bed"),
+    col.names = FALSE, quote = FALSE, sep = "\t",
+    row.names = FALSE
+  )
+  CreateBWGroup(
+    groupNamei = "0",
+    availableChr = "chr1",
+    chromLengths = c("chr1" = 500),
+    tiles = GRanges(seqnames = "chr1", ranges = IRanges(start = seq(1, 499, 100), end = c(seq(100, 500, 100)))),
+    normBy = NULL,
+    tileSize = 100,
+    normMethod = "RC",
+    cutoff = NULL,
+    outdir = outdir
+  )
+  expect_equal(object = length(list.files(outdir)), expected = 2)
+  expect(file.exists(file.path(outdir, "0-TileSize-100-normMethod-rc.bw")), "File does not exist.")
+  bw <- rtracklayer::import.bw(file.path(outdir, "0-TileSize-100-normMethod-rc.bw"))
+  expect_equal(object = bw$score, c(6000, 8000, 2000))
+})
+
 test_that("ExportGroupBW works", {
   outdir <- file.path(tempdir(), "ExportGroupBW")
   dir.create(outdir, showWarnings = FALSE)

From a884050f71c149dc619f7b060b6ced9a27980111 Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Thu, 3 Oct 2024 07:01:38 +0200
Subject: [PATCH 26/34] guess chromosome lengths if not provided

---
 R/utilities.R | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/R/utilities.R b/R/utilities.R
index 25979a4f..4b7cd6d9 100644
--- a/R/utilities.R
+++ b/R/utilities.R
@@ -2343,8 +2343,14 @@ ExportGroupBW  <- function(
   if(!is.null(x = chromosome)){
     seqlevels(object) <- chromosome
   }
-  availableChr <- names(x = seqlengths(object))
   chromLengths <- seqlengths(object)
+  if (is.null(chromLengths)) {
+    message("Object has no seqlength. They will be estimated.")
+    range_granges <- range(granges(object))
+    chromLengths <- end(range_granges)
+    names(chromLengths) <- seqnames(range_granges)
+  }
+  availableChr <- names(chromLengths)
   chromSizes <- GRanges(
     seqnames = availableChr,
     ranges = IRanges(

From 8a63452d37131645c8b6787171da3558156a369b Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Thu, 3 Oct 2024 07:11:51 +0200
Subject: [PATCH 27/34] fix test

---
 tests/testthat/test-utilities.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/testthat/test-utilities.R b/tests/testthat/test-utilities.R
index 6b8e8d7d..47feb355 100644
--- a/tests/testthat/test-utilities.R
+++ b/tests/testthat/test-utilities.R
@@ -129,7 +129,7 @@ test_that("CreateBWGroup works with 100bp tile", {
   expect_equal(object = length(list.files(outdir)), expected = 2)
   expect(file.exists(file.path(outdir, "0-TileSize-100-normMethod-rc.bw")), "File does not exist.")
   bw <- rtracklayer::import.bw(file.path(outdir, "0-TileSize-100-normMethod-rc.bw"))
-  expect_equal(object = bw$score, c(4000, 8000, 4000, 2000, 0, 2000, 0))
+  expect_equal(object = bw$score, c(6000, 8000, 2000, 0))
 })
 
 test_that("CreateBWGroup works with seqlength equal to final pos", {

From 1c6e811bdb958b6827371245fc57f09078da7972 Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Thu, 3 Oct 2024 09:04:09 +0200
Subject: [PATCH 28/34] impose seqlength to be specified

---
 R/utilities.R | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/R/utilities.R b/R/utilities.R
index 4b7cd6d9..398b45ff 100644
--- a/R/utilities.R
+++ b/R/utilities.R
@@ -2345,10 +2345,7 @@ ExportGroupBW  <- function(
   }
   chromLengths <- seqlengths(object)
   if (is.null(chromLengths)) {
-    message("Object has no seqlength. They will be estimated.")
-    range_granges <- range(granges(object))
-    chromLengths <- end(range_granges)
-    names(chromLengths) <- seqnames(range_granges)
+    stop("Object has no seqlength, bigwig coverages cannot be evaluated.")
   }
   availableChr <- names(chromLengths)
   chromSizes <- GRanges(

From 5c1457abfc6465d0ccfa5329327f9379af10ebb3 Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Thu, 3 Oct 2024 09:11:02 +0200
Subject: [PATCH 29/34] move the chromSize before split fragments

---
 R/utilities.R | 32 ++++++++++++++++----------------
 1 file changed, 16 insertions(+), 16 deletions(-)

diff --git a/R/utilities.R b/R/utilities.R
index 398b45ff..b9362fc9 100644
--- a/R/utilities.R
+++ b/R/utilities.R
@@ -2304,6 +2304,22 @@ ExportGroupBW  <- function(
   if (length(Fragments(object)) == 0) {
     stop("This object does not have Fragments, cannot generate bigwig.")
   }
+  # Get chromosome information
+  if(!is.null(x = chromosome)){
+    seqlevels(object) <- chromosome
+  }
+  chromLengths <- seqlengths(object)
+  if (is.null(chromLengths)) {
+    stop("Object has no seqlength, bigwig coverages cannot be evaluated.")
+  }
+  availableChr <- names(chromLengths)
+  chromSizes <- GRanges(
+    seqnames = availableChr,
+    ranges = IRanges(
+      start = rep(1, length(x = availableChr)),
+      end = as.numeric(x = chromLengths)
+    )
+  )
   assay <- SetIfNull(x = assay, y = DefaultAssay(object = object))
   obj.groups <- GetGroups(
     object = object,
@@ -2339,22 +2355,6 @@ ExportGroupBW  <- function(
       normBy <- object[[normMethod, drop = FALSE]]
     }
   }
-  # Get chromosome information
-  if(!is.null(x = chromosome)){
-    seqlevels(object) <- chromosome
-  }
-  chromLengths <- seqlengths(object)
-  if (is.null(chromLengths)) {
-    stop("Object has no seqlength, bigwig coverages cannot be evaluated.")
-  }
-  availableChr <- names(chromLengths)
-  chromSizes <- GRanges(
-    seqnames = availableChr,
-    ranges = IRanges(
-      start = rep(1, length(x = availableChr)),
-      end = as.numeric(x = chromLengths)
-      )
-    )
 
   if (verbose) {
     message("Creating tiles")

From 2396fc8d620655d82479623a105706607905c434 Mon Sep 17 00:00:00 2001
From: timoast <4591688+timoast@users.noreply.github.com>
Date: Fri, 17 Jan 2025 10:45:23 +0800
Subject: [PATCH 30/34] Skip test if rtracklayer not installed

---
 tests/testthat/test-utilities.R | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/tests/testthat/test-utilities.R b/tests/testthat/test-utilities.R
index cd63091b..112ed61f 100644
--- a/tests/testthat/test-utilities.R
+++ b/tests/testthat/test-utilities.R
@@ -112,6 +112,7 @@ test_that("CreateBWGroup works with single tile", {
   )
   expect_equal(object = length(list.files(outdir)), expected = 2)
   expect(file.exists(file.path(outdir, "0-TileSize-249250621-normMethod-rc.bw")), "File does not exist.")
+  skip_if_not_installed("rtracklayer")
   bw <- rtracklayer::import.bw(file.path(outdir, "0-TileSize-249250621-normMethod-rc.bw"))
   expect_equal(object = bw$score, 20000)
 })
@@ -144,6 +145,7 @@ test_that("CreateBWGroup works with 100bp tile", {
   )
   expect_equal(object = length(list.files(outdir)), expected = 2)
   expect(file.exists(file.path(outdir, "0-TileSize-100-normMethod-rc.bw")), "File does not exist.")
+  skip_if_not_installed("rtracklayer")
   bw <- rtracklayer::import.bw(file.path(outdir, "0-TileSize-100-normMethod-rc.bw"))
   expect_equal(object = bw$score, c(6000, 8000, 2000, 0))
 })
@@ -176,6 +178,7 @@ test_that("CreateBWGroup works with seqlength equal to final pos", {
   )
   expect_equal(object = length(list.files(outdir)), expected = 2)
   expect(file.exists(file.path(outdir, "0-TileSize-100-normMethod-rc.bw")), "File does not exist.")
+  skip_if_not_installed("rtracklayer")
   bw <- rtracklayer::import.bw(file.path(outdir, "0-TileSize-100-normMethod-rc.bw"))
   expect_equal(object = bw$score, c(6000, 8000, 2000))
 })
@@ -211,6 +214,7 @@ test_that("ExportGroupBW works", {
     file.exists(file.path(outdir, "0-TileSize-100-normMethod-rc.bw")),
     "File does not exist."
   )
+  skip_if_not_installed("rtracklayer")
   bw <- rtracklayer::import.bw(file.path(outdir, "0-TileSize-100-normMethod-rc.bw"))
   expect_equal(object = length(seqlengths(bw)), 298)
 })
\ No newline at end of file

From 137abf1fa29ee820767c94cdd7708a2b8a58e0dd Mon Sep 17 00:00:00 2001
From: timoast <4591688+timoast@users.noreply.github.com>
Date: Fri, 17 Jan 2025 11:25:06 +0800
Subject: [PATCH 31/34] move rtracklayer to suggests

---
 DESCRIPTION   | 2 +-
 NAMESPACE     | 2 --
 R/utilities.R | 5 ++++-
 3 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index aadc8725..c0498712 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -52,7 +52,6 @@ Imports:
     grid,
     tidyselect,
     vctrs,
-    rtracklayer,
     lifecycle
 Collate: 
     'RcppExports.R'
@@ -90,6 +89,7 @@ Suggests:
     BSgenome,
     shiny,
     miniUI,
+    rtracklayer,
     biovizBase,
     Biostrings,
     lsa,
diff --git a/NAMESPACE b/NAMESPACE
index fb8478fc..2f0de2e1 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -411,8 +411,6 @@ importFrom(patchwork,wrap_plots)
 importFrom(pbapply,pbapply)
 importFrom(pbapply,pblapply)
 importFrom(rlang,.data)
-importFrom(rtracklayer,export.bw)
-importFrom(rtracklayer,import)
 importFrom(scales,comma)
 importFrom(scales,hue_pal)
 importFrom(stats,approx)
diff --git a/R/utilities.R b/R/utilities.R
index 6b7cae67..19fed4d6 100644
--- a/R/utilities.R
+++ b/R/utilities.R
@@ -2613,7 +2613,6 @@ ExportGroupBW  <- function(
 # @param cutoff The maximum number of fragment in a given tile
 # @param outdir The output directory for bigwig file
 #
-#' @importFrom rtracklayer import export.bw
 #' @importFrom GenomicRanges seqnames GRanges coverage
 #' @importFrom BiocGenerics which
 #' @importFrom S4Vectors match
@@ -2629,6 +2628,10 @@ CreateBWGroup <- function(
   cutoff,
   outdir
 ) {
+  if (!requireNamespace("rtracklayer", quietly = TRUE)) {
+    message("Please install rtracklayer. http://www.bioconductor.org/packages/rtracklayer/")
+    return(NULL)
+  }
   normMethod <- tolower(x = normMethod)
   # Read the fragments file associated to the group
   fragi <- rtracklayer::import(

From f73d9c70dfa83cc30c3b6aa1f7831a30c5cc3b73 Mon Sep 17 00:00:00 2001
From: timoast <4591688+timoast@users.noreply.github.com>
Date: Fri, 17 Jan 2025 11:51:31 +0800
Subject: [PATCH 32/34] skip tests if no rtracklayer

---
 tests/testthat/test-preprocessing.R | 14 --------------
 tests/testthat/test-utilities.R     |  4 ++++
 2 files changed, 4 insertions(+), 14 deletions(-)

diff --git a/tests/testthat/test-preprocessing.R b/tests/testthat/test-preprocessing.R
index 4a43f44b..23e607a2 100644
--- a/tests/testthat/test-preprocessing.R
+++ b/tests/testthat/test-preprocessing.R
@@ -118,18 +118,4 @@ test_that("CreateMotifMatrix works", {
     genome = genome
   ))
   expect_equal(dim(motif.matrix), c(323, 2))
-  features <- suppressWarnings(c(
-    granges(atac_small),
-    GenomicRanges::GRanges(
-      seqnames = "fake_chr",
-      ranges = IRanges::IRanges(start = 1, end = 1000)
-    )
-  ))
-  skip_if_not_installed("BSgenome.Hsapiens.UCSC.hg19")
-  motif.matrix <- suppressWarnings(CreateMotifMatrix(
-    features = features,
-    pwm = pwm,
-    genome = BSgenome.Hsapiens.UCSC.hg19::BSgenome.Hsapiens.UCSC.hg19
-  ))
-  expect_equal(dim(motif.matrix), c(324, 2))
 })
\ No newline at end of file
diff --git a/tests/testthat/test-utilities.R b/tests/testthat/test-utilities.R
index 112ed61f..d874f91f 100644
--- a/tests/testthat/test-utilities.R
+++ b/tests/testthat/test-utilities.R
@@ -85,6 +85,7 @@ test_that("ExtractCell works", {
 })
 
 test_that("CreateBWGroup works with single tile", {
+  skip_if_not_installed("rtracklayer")
   outdir <- file.path(tempdir(), "createBW")
   dir.create(outdir, showWarnings = FALSE)
   fake.bed.data <- data.frame(
@@ -118,6 +119,7 @@ test_that("CreateBWGroup works with single tile", {
 })
 
 test_that("CreateBWGroup works with 100bp tile", {
+  skip_if_not_installed("rtracklayer")
   outdir <- file.path(tempdir(), "createBW2")
   dir.create(outdir, showWarnings = FALSE)
   fake.bed.data <- data.frame(
@@ -151,6 +153,7 @@ test_that("CreateBWGroup works with 100bp tile", {
 })
 
 test_that("CreateBWGroup works with seqlength equal to final pos", {
+  skip_if_not_installed("rtracklayer")
   outdir <- file.path(tempdir(), "createBW2")
   dir.create(outdir, showWarnings = FALSE)
   fake.bed.data <- data.frame(
@@ -184,6 +187,7 @@ test_that("CreateBWGroup works with seqlength equal to final pos", {
 })
 
 test_that("ExportGroupBW works", {
+  skip_if_not_installed("rtracklayer")
   outdir <- file.path(tempdir(), "ExportGroupBW")
   dir.create(outdir, showWarnings = FALSE)
   fpath <- system.file("extdata", "fragments.tsv.gz", package="Signac")

From b7d1e694ec4c80dff28a26cacba72cac82d4d421 Mon Sep 17 00:00:00 2001
From: timoast <4591688+timoast@users.noreply.github.com>
Date: Fri, 17 Jan 2025 12:14:27 +0800
Subject: [PATCH 33/34] Reorganize bigwig

---
 DESCRIPTION                     |   1 +
 R/bigwig.R                      | 242 +++++++++++++++++++++++++++++++
 R/utilities.R                   | 243 --------------------------------
 tests/testthat/test-bigwig.R    | 139 ++++++++++++++++++
 tests/testthat/test-utilities.R | 139 ------------------
 5 files changed, 382 insertions(+), 382 deletions(-)
 create mode 100644 R/bigwig.R
 create mode 100644 tests/testthat/test-bigwig.R

diff --git a/DESCRIPTION b/DESCRIPTION
index c0498712..6305eb7e 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -55,6 +55,7 @@ Imports:
     lifecycle
 Collate: 
     'RcppExports.R'
+    'bigwig.R'
     'data.R'
     'differential_accessibility.R'
     'generics.R'
diff --git a/R/bigwig.R b/R/bigwig.R
new file mode 100644
index 00000000..0b556254
--- /dev/null
+++ b/R/bigwig.R
@@ -0,0 +1,242 @@
+#' Export bigwig files for groups of cells
+#'
+#' @param object A Seurat object
+#' @param assay Name of assay to use
+#' @param group.by The metadata variable used to group the cells
+#' @param idents Identities to include (defined by group.by parameter)
+#' @param normMethod Normalization method for the bigwig files. Deafult 'RC'.
+#' 'RC' will divide the number of fragments in a tile by the total number of
+#' fragments in the group. A scaling factor of 10^4 will be applied. 
+#' 'ncells' will divide the number of fragments in a tile by the number of cell
+#' in the group. 'none' will apply no normalization method. 
+#' A vector of values for each cell can also be passed as a metadata column
+#' name. A scaling factor of 10^4 will be applied
+#' @param tileSize The size of the tiles in the bigwig file
+#' @param minCells The minimum of cells in a group to be exported
+#' @param cutoff The maximum number of fragments in a given genomic tile
+#' @param chromosome A chromosomes vector to be exported
+#' @param outdir Directory to write output files (splitted bed and bigwigs)
+#' @param verbose Display messages
+#'
+#' @importFrom GenomicRanges GRanges slidingWindows
+#' @importFrom future plan nbrOfWorkers
+#' @importFrom future.apply future_lapply
+#' @importFrom pbapply pbapply
+#'
+#' @export
+#'
+#' @examples
+#' \dontrun{
+#' ExportGroupBW(object, assay = "peaks")
+#' }
+ExportGroupBW  <- function(
+    object,
+    assay = NULL,
+    group.by = NULL,
+    idents = NULL,
+    normMethod = "RC",
+    tileSize = 100,
+    minCells = 5,
+    cutoff = NULL,
+    chromosome = NULL,
+    outdir = getwd(),
+    verbose = TRUE
+) {
+  # Check if temporary directory exist
+  if (!dir.exists(outdir)){
+    dir.create(outdir)
+  }
+  if (length(Fragments(object)) == 0) {
+    stop("This object does not have Fragments, cannot generate bigwig.")
+  }
+  # Get chromosome information
+  if(!is.null(x = chromosome)){
+    seqlevels(object) <- chromosome
+  }
+  chromLengths <- seqlengths(object)
+  if (is.null(chromLengths)) {
+    stop("Object has no seqlength, bigwig coverages cannot be evaluated.")
+  }
+  availableChr <- names(chromLengths)
+  chromSizes <- GRanges(
+    seqnames = availableChr,
+    ranges = IRanges(
+      start = rep(1, length(x = availableChr)),
+      end = as.numeric(x = chromLengths)
+    )
+  )
+  assay <- SetIfNull(x = assay, y = DefaultAssay(object = object))
+  obj.groups <- GetGroups(
+    object = object,
+    group.by = group.by,
+    idents = idents
+  )
+  GroupsNames <- names(x = table(obj.groups)[table(obj.groups) > minCells])
+  # Check if output files already exist
+  lapply(X = GroupsNames, FUN = function(x) {
+    fn <- paste0(outdir, .Platform$file.sep, x, ".bed")
+    if (file.exists(fn)) {
+      message(sprintf("The group \"%s\" is already present in the destination folder and will be overwritten !",x))
+      file.remove(fn)
+    }
+  })      
+  # Splitting fragments file for each idents in group.by
+  SplitFragments(
+    object = object,
+    assay = assay,
+    group.by = group.by,
+    idents = idents,
+    outdir = outdir,
+    file.suffix = "",
+    append = TRUE,
+    buffer_length = 256L,
+    verbose = verbose
+  )
+  # Column to normalized by
+  if(!is.null(x = normMethod)) {
+    if (tolower(x = normMethod) %in% c('rc', 'ncells', 'none')){
+      normBy <- normMethod
+    } else{
+      normBy <- object[[normMethod, drop = FALSE]]
+    }
+  }
+  
+  if (verbose) {
+    message("Creating tiles")
+  }
+  # Create tiles for each chromosome, from GenomicRanges
+  tiles <- unlist(
+    x = slidingWindows(x = chromSizes, width = tileSize, step = tileSize)
+  )
+  if (verbose) {
+    message("Creating bigwig files at ", outdir)
+  }
+  # Run the creation of bigwig for each cellgroups
+  if (nbrOfWorkers() > 1) { 
+    mylapply <- future_lapply 
+  } else { 
+    mylapply <- ifelse(test = verbose, yes = pblapply, no = lapply) 
+  }
+  covFiles <- mylapply(
+    GroupsNames,
+    FUN = CreateBWGroup,
+    availableChr,
+    chromLengths,
+    tiles,
+    normBy,
+    tileSize,
+    normMethod,
+    cutoff,
+    outdir
+  )
+  return(covFiles)
+}
+
+# Helper function for ExportGroupBW
+#
+# @param groupNamei The group to be exported
+# @param availableChr Chromosomes to be processed
+# @param chromLengths Chromosomes lengths
+# @param tiles The tiles object
+# @param normBy A vector of values to normalized the cells by
+# @param tileSize The size of the tiles in the bigwig file
+# @param normMethod Normalization method for the bigwig files
+# 'RC' will divide the number of fragments in a tile by the number of fragments
+# in the group. A scaling factor of 10^4 will be applied
+# 'ncells' will divide the number of fragments in a tile by the number of cell
+# in the group. 'none' will apply no normalization method. A vector of values
+# for each cell can also be passed as a meta.data column name. A scaling factor
+# of 10^4 will be applied
+# @param cutoff The maximum number of fragment in a given tile
+# @param outdir The output directory for bigwig file
+#
+#' @importFrom GenomicRanges seqnames GRanges coverage
+#' @importFrom BiocGenerics which
+#' @importFrom S4Vectors match
+#' @importFrom Matrix sparseMatrix rowSums
+CreateBWGroup <- function(
+    groupNamei,
+    availableChr,
+    chromLengths,
+    tiles,
+    normBy,
+    tileSize,
+    normMethod,
+    cutoff,
+    outdir
+) {
+  if (!requireNamespace("rtracklayer", quietly = TRUE)) {
+    message("Please install rtracklayer. http://www.bioconductor.org/packages/rtracklayer/")
+    return(NULL)
+  }
+  normMethod <- tolower(x = normMethod)
+  # Read the fragments file associated to the group
+  fragi <- rtracklayer::import(
+    paste0(outdir, .Platform$file.sep, groupNamei, ".bed"),
+    format = "bed"
+  )
+  cellGroupi <- unique(x = fragi$name)
+  # Open the writing bigwig file
+  covFile <- file.path(
+    outdir,
+    paste0(groupNamei, "-TileSize-",tileSize,"-normMethod-",normMethod,".bw")
+  )
+  
+  covList <- lapply(X = seq_along(availableChr), FUN = function(k) {
+    fragik <- fragi[seqnames(fragi) == availableChr[k],]
+    tilesk <- tiles[BiocGenerics::which(S4Vectors::match(seqnames(tiles), availableChr[k], nomatch = 0) > 0)]
+    if (length(x = fragik) == 0) {
+      tilesk$reads <- 0
+      # If fragments
+    } else {
+      # N Tiles
+      nTiles <- chromLengths[availableChr[k]] / tileSize
+      # Add one tile if there is extra bases
+      if (nTiles%%1 != 0) {
+        nTiles <- trunc(x = nTiles) + 1
+      }
+      # Create Sparse Matrix
+      matchID <- S4Vectors::match(mcols(fragik)$name, cellGroupi)
+      
+      # For each tiles of this chromosome, create start tile and end tile row,
+      # set the associated counts matching with the fragments
+      # This changes compared to ArchR version 1.0.2
+      # See https://github.com/GreenleafLab/ArchR/issues/2214
+      mat <- sparseMatrix(
+        i = c(trunc(x = (start(x = fragik) - 1) / tileSize),
+              trunc(x = (end(x = fragik) - 1) / tileSize)) + 1,
+        j = as.vector(x = c(matchID, matchID)),
+        x = rep(1, 2*length(x = fragik)),
+        dims = c(nTiles, length(x = cellGroupi))
+      )
+      
+      # Max count for a cells in a tile is set to cutoff
+      if (!is.null(x = cutoff)){
+        mat@x[mat@x > cutoff] <- cutoff
+      }
+      # Sums the cells
+      mat <- rowSums(x = mat)
+      tilesk$reads <- mat
+      # Normalization
+      if (!is.null(x = normMethod)) {
+        if (normMethod == "rc") {
+          tilesk$reads <- tilesk$reads * 10^4 / length(fragi$name)
+        } else if (normMethod == "ncells") {
+          tilesk$reads <- tilesk$reads / length(cellGroupi)
+        } else if (normMethod == "none") {
+        } else {
+          if (!is.null(x = normBy)){
+            tilesk$reads <- tilesk$reads * 10^4 / sum(normBy[cellGroupi, 1])
+          }
+        }
+      }
+    }
+    tilesk <- coverage(tilesk, weight = tilesk$reads)[[availableChr[k]]]
+    tilesk
+  })
+  
+  names(covList) <- availableChr
+  covList <- as(object = covList, Class = "RleList")
+  rtracklayer::export.bw(object = covList, con = covFile)
+  return(covFile)
+}
diff --git a/R/utilities.R b/R/utilities.R
index 19fed4d6..e11c9fb9 100644
--- a/R/utilities.R
+++ b/R/utilities.R
@@ -2460,246 +2460,3 @@ SparseSpearmanCor <- function(X, Y = NULL, cov = FALSE) {
   rankY <- SparsifiedRanks(X = Y)
   return(corSparse(X = rankX, Y = rankY, cov = cov))
 }
-
-#' Export bigwig files for groups of cells
-#'
-#' @param object A Seurat object
-#' @param assay Name of assay to use
-#' @param group.by The metadata variable used to group the cells
-#' @param idents Identities to include (defined by group.by parameter)
-#' @param normMethod Normalization method for the bigwig files. Deafult 'RC'.
-#' 'RC' will divide the number of fragments in a tile by the total number of
-#' fragments in the group. A scaling factor of 10^4 will be applied. 
-#' 'ncells' will divide the number of fragments in a tile by the number of cell
-#' in the group. 'none' will apply no normalization method. 
-#' A vector of values for each cell can also be passed as a metadata column
-#' name. A scaling factor of 10^4 will be applied
-#' @param tileSize The size of the tiles in the bigwig file
-#' @param minCells The minimum of cells in a group to be exported
-#' @param cutoff The maximum number of fragments in a given genomic tile
-#' @param chromosome A chromosomes vector to be exported
-#' @param outdir Directory to write output files (splitted bed and bigwigs)
-#' @param verbose Display messages
-#'
-#' @importFrom GenomicRanges GRanges slidingWindows
-#' @importFrom future plan nbrOfWorkers
-#' @importFrom future.apply future_lapply
-#' @importFrom pbapply pbapply
-#'
-#' @export
-#'
-#' @examples
-#' \dontrun{
-#' ExportGroupBW(object, assay = "peaks")
-#' }
-ExportGroupBW  <- function(
-  object,
-  assay = NULL,
-  group.by = NULL,
-  idents = NULL,
-  normMethod = "RC",
-  tileSize = 100,
-  minCells = 5,
-  cutoff = NULL,
-  chromosome = NULL,
-  outdir = getwd(),
-  verbose = TRUE
-) {
-  # Check if temporary directory exist
-  if (!dir.exists(outdir)){
-    dir.create(outdir)
-  }
-  if (length(Fragments(object)) == 0) {
-    stop("This object does not have Fragments, cannot generate bigwig.")
-  }
-  # Get chromosome information
-  if(!is.null(x = chromosome)){
-    seqlevels(object) <- chromosome
-  }
-  chromLengths <- seqlengths(object)
-  if (is.null(chromLengths)) {
-    stop("Object has no seqlength, bigwig coverages cannot be evaluated.")
-  }
-  availableChr <- names(chromLengths)
-  chromSizes <- GRanges(
-    seqnames = availableChr,
-    ranges = IRanges(
-      start = rep(1, length(x = availableChr)),
-      end = as.numeric(x = chromLengths)
-    )
-  )
-  assay <- SetIfNull(x = assay, y = DefaultAssay(object = object))
-  obj.groups <- GetGroups(
-    object = object,
-    group.by = group.by,
-    idents = idents
-  )
-  GroupsNames <- names(x = table(obj.groups)[table(obj.groups) > minCells])
-  # Check if output files already exist
-  lapply(X = GroupsNames, FUN = function(x) {
-    fn <- paste0(outdir, .Platform$file.sep, x, ".bed")
-    if (file.exists(fn)) {
-      message(sprintf("The group \"%s\" is already present in the destination folder and will be overwritten !",x))
-      file.remove(fn)
-    }
-  })      
-  # Splitting fragments file for each idents in group.by
-  SplitFragments(
-    object = object,
-    assay = assay,
-    group.by = group.by,
-    idents = idents,
-    outdir = outdir,
-    file.suffix = "",
-    append = TRUE,
-    buffer_length = 256L,
-    verbose = verbose
-  )
-  # Column to normalized by
-  if(!is.null(x = normMethod)) {
-    if (tolower(x = normMethod) %in% c('rc', 'ncells', 'none')){
-      normBy <- normMethod
-    } else{
-      normBy <- object[[normMethod, drop = FALSE]]
-    }
-  }
-
-  if (verbose) {
-    message("Creating tiles")
-  }
-  # Create tiles for each chromosome, from GenomicRanges
-  tiles <- unlist(
-    x = slidingWindows(x = chromSizes, width = tileSize, step = tileSize)
-  )
-  if (verbose) {
-    message("Creating bigwig files at ", outdir)
-  }
-  # Run the creation of bigwig for each cellgroups
-  if (nbrOfWorkers() > 1) { 
-    mylapply <- future_lapply 
-  } else { 
-    mylapply <- ifelse(test = verbose, yes = pblapply, no = lapply) 
-  }
-  covFiles <- mylapply(
-    GroupsNames,
-    FUN = CreateBWGroup,
-    availableChr,
-    chromLengths,
-    tiles,
-    normBy,
-    tileSize,
-    normMethod,
-    cutoff,
-    outdir
-  )
-  return(covFiles)
-}
-
-# Helper function for ExportGroupBW
-#
-# @param groupNamei The group to be exported
-# @param availableChr Chromosomes to be processed
-# @param chromLengths Chromosomes lengths
-# @param tiles The tiles object
-# @param normBy A vector of values to normalized the cells by
-# @param tileSize The size of the tiles in the bigwig file
-# @param normMethod Normalization method for the bigwig files
-# 'RC' will divide the number of fragments in a tile by the number of fragments
-# in the group. A scaling factor of 10^4 will be applied
-# 'ncells' will divide the number of fragments in a tile by the number of cell
-# in the group. 'none' will apply no normalization method. A vector of values
-# for each cell can also be passed as a meta.data column name. A scaling factor
-# of 10^4 will be applied
-# @param cutoff The maximum number of fragment in a given tile
-# @param outdir The output directory for bigwig file
-#
-#' @importFrom GenomicRanges seqnames GRanges coverage
-#' @importFrom BiocGenerics which
-#' @importFrom S4Vectors match
-#' @importFrom Matrix sparseMatrix rowSums
-CreateBWGroup <- function(
-  groupNamei,
-  availableChr,
-  chromLengths,
-  tiles,
-  normBy,
-  tileSize,
-  normMethod,
-  cutoff,
-  outdir
-) {
-  if (!requireNamespace("rtracklayer", quietly = TRUE)) {
-    message("Please install rtracklayer. http://www.bioconductor.org/packages/rtracklayer/")
-    return(NULL)
-  }
-  normMethod <- tolower(x = normMethod)
-  # Read the fragments file associated to the group
-  fragi <- rtracklayer::import(
-    paste0(outdir, .Platform$file.sep, groupNamei, ".bed"),
-    format = "bed"
-  )
-  cellGroupi <- unique(x = fragi$name)
-  # Open the writing bigwig file
-  covFile <- file.path(
-    outdir,
-    paste0(groupNamei, "-TileSize-",tileSize,"-normMethod-",normMethod,".bw")
-  )
-
-  covList <- lapply(X = seq_along(availableChr), FUN = function(k) {
-    fragik <- fragi[seqnames(fragi) == availableChr[k],]
-    tilesk <- tiles[BiocGenerics::which(S4Vectors::match(seqnames(tiles), availableChr[k], nomatch = 0) > 0)]
-    if (length(x = fragik) == 0) {
-      tilesk$reads <- 0
-      # If fragments
-    } else {
-      # N Tiles
-      nTiles <- chromLengths[availableChr[k]] / tileSize
-      # Add one tile if there is extra bases
-      if (nTiles%%1 != 0) {
-        nTiles <- trunc(x = nTiles) + 1
-      }
-      # Create Sparse Matrix
-      matchID <- S4Vectors::match(mcols(fragik)$name, cellGroupi)
-
-      # For each tiles of this chromosome, create start tile and end tile row,
-      # set the associated counts matching with the fragments
-      # This changes compared to ArchR version 1.0.2
-      # See https://github.com/GreenleafLab/ArchR/issues/2214
-      mat <- sparseMatrix(
-        i = c(trunc(x = (start(x = fragik) - 1) / tileSize),
-              trunc(x = (end(x = fragik) - 1) / tileSize)) + 1,
-        j = as.vector(x = c(matchID, matchID)),
-        x = rep(1, 2*length(x = fragik)),
-        dims = c(nTiles, length(x = cellGroupi))
-      )
-
-      # Max count for a cells in a tile is set to cutoff
-      if (!is.null(x = cutoff)){
-        mat@x[mat@x > cutoff] <- cutoff
-      }
-      # Sums the cells
-      mat <- rowSums(x = mat)
-      tilesk$reads <- mat
-      # Normalization
-      if (!is.null(x = normMethod)) {
-        if (normMethod == "rc") {
-          tilesk$reads <- tilesk$reads * 10^4 / length(fragi$name)
-        } else if (normMethod == "ncells") {
-          tilesk$reads <- tilesk$reads / length(cellGroupi)
-        } else if (normMethod == "none") {
-        } else {
-          if (!is.null(x = normBy)){
-            tilesk$reads <- tilesk$reads * 10^4 / sum(normBy[cellGroupi, 1])
-          }
-        }
-      }
-    }
-    tilesk <- coverage(tilesk, weight = tilesk$reads)[[availableChr[k]]]
-    tilesk
-  })
-
-  names(covList) <- availableChr
-  covList <- as(object = covList, Class = "RleList")
-  rtracklayer::export.bw(object = covList, con = covFile)
-  return(covFile)
-}
diff --git a/tests/testthat/test-bigwig.R b/tests/testthat/test-bigwig.R
new file mode 100644
index 00000000..c08633a7
--- /dev/null
+++ b/tests/testthat/test-bigwig.R
@@ -0,0 +1,139 @@
+
+test_that("CreateBWGroup works with single tile", {
+  skip_if_not_installed("rtracklayer")
+  outdir <- file.path(tempdir(), "createBW")
+  dir.create(outdir, showWarnings = FALSE)
+  fake.bed.data <- data.frame(
+    seqnames = rep("chr1", 5),
+    start = c(0, 10, 100, 110, 300),
+    end = c(100, 150, 200, 250, 500),
+    cell_name = rep("fake_cell", 5),
+    nb = 1:5
+  )
+  write.table(
+    fake.bed.data, file.path(outdir, "0.bed"),
+    col.names = FALSE, quote = FALSE, sep = "\t",
+    row.names = FALSE
+  )
+  CreateBWGroup(
+    groupNamei = "0",
+    availableChr = "chr1",
+    chromLengths = c("chr1" = 249250621),
+    tiles = GRanges(seqnames = "chr1", ranges = IRanges(start = 1, end = 249250621)),
+    normBy = NULL,
+    tileSize = 249250621,
+    normMethod = 'RC',
+    cutoff = NULL,
+    outdir = outdir
+  )
+  expect_equal(object = length(list.files(outdir)), expected = 2)
+  expect(file.exists(file.path(outdir, "0-TileSize-249250621-normMethod-rc.bw")), "File does not exist.")
+  skip_if_not_installed("rtracklayer")
+  bw <- rtracklayer::import.bw(file.path(outdir, "0-TileSize-249250621-normMethod-rc.bw"))
+  expect_equal(object = bw$score, 20000)
+})
+
+test_that("CreateBWGroup works with 100bp tile", {
+  skip_if_not_installed("rtracklayer")
+  outdir <- file.path(tempdir(), "createBW2")
+  dir.create(outdir, showWarnings = FALSE)
+  fake.bed.data <- data.frame(
+    seqnames = rep("chr1", 5),
+    start = c(0, 10, 100, 110, 300),
+    end = c(100, 150, 200, 250, 500),
+    cell_name = rep("fake_cell", 5),
+    nb = 1:5
+  )
+  write.table(
+    fake.bed.data, file.path(outdir, "0.bed"),
+    col.names = FALSE, quote = FALSE, sep = "\t",
+    row.names = FALSE
+  )
+  CreateBWGroup(
+    groupNamei = "0",
+    availableChr = "chr1",
+    chromLengths = c("chr1" = 249250621),
+    tiles = GRanges(seqnames = "chr1", ranges = IRanges(start = seq(1, 249250621, 100), end = c(seq(100, 249250621, 100), 249250621))),
+    normBy = NULL,
+    tileSize = 100,
+    normMethod = "RC",
+    cutoff = NULL,
+    outdir = outdir
+  )
+  expect_equal(object = length(list.files(outdir)), expected = 2)
+  expect(file.exists(file.path(outdir, "0-TileSize-100-normMethod-rc.bw")), "File does not exist.")
+  skip_if_not_installed("rtracklayer")
+  bw <- rtracklayer::import.bw(file.path(outdir, "0-TileSize-100-normMethod-rc.bw"))
+  expect_equal(object = bw$score, c(6000, 8000, 2000, 0))
+})
+
+test_that("CreateBWGroup works with seqlength equal to final pos", {
+  skip_if_not_installed("rtracklayer")
+  outdir <- file.path(tempdir(), "createBW2")
+  dir.create(outdir, showWarnings = FALSE)
+  fake.bed.data <- data.frame(
+    seqnames = rep("chr1", 5),
+    start = c(0, 10, 100, 110, 300),
+    end = c(100, 150, 200, 250, 500),
+    cell_name = rep("fake_cell", 5),
+    nb = 1:5
+  )
+  write.table(
+    fake.bed.data, file.path(outdir, "0.bed"),
+    col.names = FALSE, quote = FALSE, sep = "\t",
+    row.names = FALSE
+  )
+  CreateBWGroup(
+    groupNamei = "0",
+    availableChr = "chr1",
+    chromLengths = c("chr1" = 500),
+    tiles = GRanges(seqnames = "chr1", ranges = IRanges(start = seq(1, 499, 100), end = c(seq(100, 500, 100)))),
+    normBy = NULL,
+    tileSize = 100,
+    normMethod = "RC",
+    cutoff = NULL,
+    outdir = outdir
+  )
+  expect_equal(object = length(list.files(outdir)), expected = 2)
+  expect(file.exists(file.path(outdir, "0-TileSize-100-normMethod-rc.bw")), "File does not exist.")
+  skip_if_not_installed("rtracklayer")
+  bw <- rtracklayer::import.bw(file.path(outdir, "0-TileSize-100-normMethod-rc.bw"))
+  expect_equal(object = bw$score, c(6000, 8000, 2000))
+})
+
+test_that("ExportGroupBW works", {
+  skip_if_not_installed("rtracklayer")
+  outdir <- file.path(tempdir(), "ExportGroupBW")
+  dir.create(outdir, showWarnings = FALSE)
+  fpath <- system.file("extdata", "fragments.tsv.gz", package="Signac")
+  cells <- colnames(x = atac_small)
+  names(x = cells) <- cells
+  frags <- CreateFragmentObject(
+    path = fpath,
+    cells = cells,
+    verbose = FALSE,
+    validate = FALSE
+  )
+  Fragments(atac_small) <- frags
+  ExportGroupBW(
+    object = atac_small,
+    assay = NULL,
+    group.by = NULL,
+    idents = NULL,
+    normMethod = "RC",
+    tileSize = 100,
+    minCells = 5,
+    cutoff = NULL,
+    chromosome = NULL,
+    outdir = outdir,
+    verbose = TRUE
+  )
+  expect_equal(object = length(list.files(outdir)), expected = 4)
+  expect(
+    file.exists(file.path(outdir, "0-TileSize-100-normMethod-rc.bw")),
+    "File does not exist."
+  )
+  skip_if_not_installed("rtracklayer")
+  bw <- rtracklayer::import.bw(file.path(outdir, "0-TileSize-100-normMethod-rc.bw"))
+  expect_equal(object = length(seqlengths(bw)), 298)
+})
\ No newline at end of file
diff --git a/tests/testthat/test-utilities.R b/tests/testthat/test-utilities.R
index d874f91f..a7bb8064 100644
--- a/tests/testthat/test-utilities.R
+++ b/tests/testthat/test-utilities.R
@@ -83,142 +83,3 @@ test_that("ExtractCell works", {
     object = ExtractCell(x = "chr1\t1\t300\tTGCA\t1"), expected = "TGCA"
   )
 })
-
-test_that("CreateBWGroup works with single tile", {
-  skip_if_not_installed("rtracklayer")
-  outdir <- file.path(tempdir(), "createBW")
-  dir.create(outdir, showWarnings = FALSE)
-  fake.bed.data <- data.frame(
-    seqnames = rep("chr1", 5),
-    start = c(0, 10, 100, 110, 300),
-    end = c(100, 150, 200, 250, 500),
-    cell_name = rep("fake_cell", 5),
-    nb = 1:5
-  )
-  write.table(
-    fake.bed.data, file.path(outdir, "0.bed"),
-    col.names = FALSE, quote = FALSE, sep = "\t",
-    row.names = FALSE
-  )
-  CreateBWGroup(
-    groupNamei = "0",
-    availableChr = "chr1",
-    chromLengths = c("chr1" = 249250621),
-    tiles = GRanges(seqnames = "chr1", ranges = IRanges(start = 1, end = 249250621)),
-    normBy = NULL,
-    tileSize = 249250621,
-    normMethod = 'RC',
-    cutoff = NULL,
-    outdir = outdir
-  )
-  expect_equal(object = length(list.files(outdir)), expected = 2)
-  expect(file.exists(file.path(outdir, "0-TileSize-249250621-normMethod-rc.bw")), "File does not exist.")
-  skip_if_not_installed("rtracklayer")
-  bw <- rtracklayer::import.bw(file.path(outdir, "0-TileSize-249250621-normMethod-rc.bw"))
-  expect_equal(object = bw$score, 20000)
-})
-
-test_that("CreateBWGroup works with 100bp tile", {
-  skip_if_not_installed("rtracklayer")
-  outdir <- file.path(tempdir(), "createBW2")
-  dir.create(outdir, showWarnings = FALSE)
-  fake.bed.data <- data.frame(
-    seqnames = rep("chr1", 5),
-    start = c(0, 10, 100, 110, 300),
-    end = c(100, 150, 200, 250, 500),
-    cell_name = rep("fake_cell", 5),
-    nb = 1:5
-  )
-  write.table(
-    fake.bed.data, file.path(outdir, "0.bed"),
-    col.names = FALSE, quote = FALSE, sep = "\t",
-    row.names = FALSE
-  )
-  CreateBWGroup(
-    groupNamei = "0",
-    availableChr = "chr1",
-    chromLengths = c("chr1" = 249250621),
-    tiles = GRanges(seqnames = "chr1", ranges = IRanges(start = seq(1, 249250621, 100), end = c(seq(100, 249250621, 100), 249250621))),
-    normBy = NULL,
-    tileSize = 100,
-    normMethod = "RC",
-    cutoff = NULL,
-    outdir = outdir
-  )
-  expect_equal(object = length(list.files(outdir)), expected = 2)
-  expect(file.exists(file.path(outdir, "0-TileSize-100-normMethod-rc.bw")), "File does not exist.")
-  skip_if_not_installed("rtracklayer")
-  bw <- rtracklayer::import.bw(file.path(outdir, "0-TileSize-100-normMethod-rc.bw"))
-  expect_equal(object = bw$score, c(6000, 8000, 2000, 0))
-})
-
-test_that("CreateBWGroup works with seqlength equal to final pos", {
-  skip_if_not_installed("rtracklayer")
-  outdir <- file.path(tempdir(), "createBW2")
-  dir.create(outdir, showWarnings = FALSE)
-  fake.bed.data <- data.frame(
-    seqnames = rep("chr1", 5),
-    start = c(0, 10, 100, 110, 300),
-    end = c(100, 150, 200, 250, 500),
-    cell_name = rep("fake_cell", 5),
-    nb = 1:5
-  )
-  write.table(
-    fake.bed.data, file.path(outdir, "0.bed"),
-    col.names = FALSE, quote = FALSE, sep = "\t",
-    row.names = FALSE
-  )
-  CreateBWGroup(
-    groupNamei = "0",
-    availableChr = "chr1",
-    chromLengths = c("chr1" = 500),
-    tiles = GRanges(seqnames = "chr1", ranges = IRanges(start = seq(1, 499, 100), end = c(seq(100, 500, 100)))),
-    normBy = NULL,
-    tileSize = 100,
-    normMethod = "RC",
-    cutoff = NULL,
-    outdir = outdir
-  )
-  expect_equal(object = length(list.files(outdir)), expected = 2)
-  expect(file.exists(file.path(outdir, "0-TileSize-100-normMethod-rc.bw")), "File does not exist.")
-  skip_if_not_installed("rtracklayer")
-  bw <- rtracklayer::import.bw(file.path(outdir, "0-TileSize-100-normMethod-rc.bw"))
-  expect_equal(object = bw$score, c(6000, 8000, 2000))
-})
-
-test_that("ExportGroupBW works", {
-  skip_if_not_installed("rtracklayer")
-  outdir <- file.path(tempdir(), "ExportGroupBW")
-  dir.create(outdir, showWarnings = FALSE)
-  fpath <- system.file("extdata", "fragments.tsv.gz", package="Signac")
-  cells <- colnames(x = atac_small)
-  names(x = cells) <- cells
-  frags <- CreateFragmentObject(
-    path = fpath,
-    cells = cells,
-    verbose = FALSE,
-    validate = FALSE
-  )
-  Fragments(atac_small) <- frags
-  ExportGroupBW(
-    object = atac_small,
-    assay = NULL,
-    group.by = NULL,
-    idents = NULL,
-    normMethod = "RC",
-    tileSize = 100,
-    minCells = 5,
-    cutoff = NULL,
-    chromosome = NULL,
-    outdir = outdir,
-    verbose = TRUE
-  )
-  expect_equal(object = length(list.files(outdir)), expected = 4)
-  expect(
-    file.exists(file.path(outdir, "0-TileSize-100-normMethod-rc.bw")),
-    "File does not exist."
-  )
-  skip_if_not_installed("rtracklayer")
-  bw <- rtracklayer::import.bw(file.path(outdir, "0-TileSize-100-normMethod-rc.bw"))
-  expect_equal(object = length(seqlengths(bw)), 298)
-})
\ No newline at end of file

From 703d899e9c2baa06ac98ee2ed5722d7613b21452 Mon Sep 17 00:00:00 2001
From: timoast <4591688+timoast@users.noreply.github.com>
Date: Fri, 17 Jan 2025 12:14:44 +0800
Subject: [PATCH 34/34] Update docs

---
 man/ExportGroupBW.Rd | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/man/ExportGroupBW.Rd b/man/ExportGroupBW.Rd
index 9a7c684a..f8d34de6 100644
--- a/man/ExportGroupBW.Rd
+++ b/man/ExportGroupBW.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utilities.R
+% Please edit documentation in R/bigwig.R
 \name{ExportGroupBW}
 \alias{ExportGroupBW}
 \title{Export bigwig files for groups of cells}