1.1.17

DiseaseNeuroGenomics · Feb 13, 2024 · 8019df8 · 8019df8
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diff --git a/NEWS.md b/NEWS.md
@@ -1,6 +1,8 @@
 
 # dreamlet 1.1.17
-  - bug fix in `plotPCA()`
+  - new functionality in `plotPCA()` and `outlierByAssay()` 
+   - works on any `list`, not just `dreamletProcessedData`
+   - allows outlier analysis on residuals
 
 # dreamlet 1.1.16
   - Feb 8, 2024

diff --git a/R/dreamletProcessedData.R b/R/dreamletProcessedData.R
@@ -448,3 +448,4 @@ setMethod(
     list(assayLevel = df, geneLevel = df2)
   }
 )
+
diff --git a/R/outlier.R b/R/outlier.R
@@ -92,11 +92,16 @@ outlier <- function(data, robust = FALSE, ...) {
 #' @export
 outlierByAssay = function(object, assays = assayNames(object), nPC=2, robust = FALSE, ...){
 
-  stopifnot(is(object, "dreamletProcessedData"))
+  stopifnot(is(object, "list"))
 
    df = lapply(assays, function(id){
     # get normalized expression
-    Y <- assay(object, id)$E
+    # Y <- assay(object, id)$E
+    if( is(object[[id]], "EList") ){
+      Y <- object[[id]]$E
+    }else{
+      Y <- object[[id]]
+    }
 
     # PCA
     # dcmp <- prcomp(scale(t(Y)))

diff --git a/R/plotPCA.R b/R/plotPCA.R
@@ -8,7 +8,7 @@ setGeneric("plotPCA", BiocGenerics::plotPCA)
 #' 
 #' Compute PCA of gene expression for an assay, and plot samples coloring by outlier score
 #' 
-#' @param object \code{dreamletProcessedData} from \code{processAssays()}
+#' @param object \code{dreamletProcessedData} from \code{processAssays()} or a \code{list} from \code{residuals()}
 #' @param assays assays / cell types to analyze
 #' @param nPC number of PCs to uses for outlier score with \code{outlier()}
 #' @param robust use robust covariance method, defaults to \code{FALSE}
@@ -20,7 +20,7 @@ setGeneric("plotPCA", BiocGenerics::plotPCA)
 #' 
 #' @name plotPCA
 #' @rdname plotPCA
-#' @aliases plotPCA plotPCA,dreamletProcessedData-method
+#' @aliases plotPCA plotPCA,list-method
 #' @examples
 #' library(muscat)
 #' library(SingleCellExperiment)
@@ -39,13 +39,26 @@ setGeneric("plotPCA", BiocGenerics::plotPCA)
 #' res.proc <- processAssays(pb, ~group_id)
 #' 
 #' # PCA to identify outliers
-#' plotPCA( res.proc, "CD14+ Monocytes")
+#' # from normalized expression
+#' plotPCA( res.proc, c("B cells", "CD14+ Monocytes"))
+#'
+#' # Run on regression residuals
+#' #-----------------------------
+#'
+#' # Regression analysis
+#' fit = dreamlet(res.proc, ~ group_id)
+#' 
+#' # Extract regression residuals
+#' residsObj = residuals(fit)
+#' 
+#' # PCA on residuals
+#' plotPCA( residsObj, c("B cells", "CD14+ Monocytes"))
 #
 #' @seealso \code{outlierByAssay()}
 #' @export
-setMethod("plotPCA", signature(object="dreamletProcessedData"), function(object, assays = assayNames(object), nPC=2, robust = FALSE, ..., maxOutlierZ=20, nrow=2, size=2, fdr.cutoff=0.05){
+setMethod("plotPCA", signature(object="list"), function(object, assays = names(object), nPC=2, robust = FALSE, ..., maxOutlierZ=20, nrow=2, size=2, fdr.cutoff=0.05){
 
-  stopifnot(all(assays %in% assayNames(object)))
+  stopifnot(all(assays %in% names(object)))
 
   PC1 <- PC2 <- z <- pValue <- FDR <- NULL
 
@@ -64,3 +77,10 @@ setMethod("plotPCA", signature(object="dreamletProcessedData"), function(object,
 })
 
 
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diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/authors.html b/docs/authors.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/news/index.html b/docs/news/index.html
diff --git a/docs/reference/Rplot001.png b/docs/reference/Rplot001.png
diff --git a/docs/reference/Rplot002.png b/docs/reference/Rplot002.png
diff --git a/docs/reference/index.html b/docs/reference/index.html
diff --git a/docs/reference/plotPCA-1.png b/docs/reference/plotPCA-1.png
diff --git a/docs/reference/plotPCA-2.png b/docs/reference/plotPCA-2.png
diff --git a/docs/reference/plotPCA.html b/docs/reference/plotPCA.html
diff --git a/man/plotPCA.Rd b/man/plotPCA.Rd
Original file line number	Diff line number	Diff line change
Expand Up		@@ -448,3 +448,4 @@ setMethod(
		list(assayLevel = df, geneLevel = df2)
		}
		)