From 69eb8fa98d5bde337e8d5f045a4eb566c9d3036e Mon Sep 17 00:00:00 2001
From: pcamara <pablo.g.camara@gmail.com>
Date: Tue, 6 Feb 2024 12:54:54 -0500
Subject: [PATCH] Improved AdjScoreHeatmap

---
 DESCRIPTION        |  1 +
 NAMESPACE          |  1 +
 R/feature_scores.R | 17 +++++++++++++----
 3 files changed, 15 insertions(+), 4 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 468b462..7c39de6 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -21,6 +21,7 @@ Imports:
     Matrix,
     mclust,
     methods,
+    pheatmap,
     RANN,
     stringr,
     tidyr
diff --git a/NAMESPACE b/NAMESPACE
index ebb78c9..f1afdbb 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -59,6 +59,7 @@ import(AdjacencyScore)
 import(Matrix)
 import(ggplot2)
 import(mclust)
+import(pheatmap)
 importFrom(RANN,nn2)
 importFrom(cluster,silhouette)
 importFrom(colorspace,rainbow_hcl)
diff --git a/R/feature_scores.R b/R/feature_scores.R
index cedaafe..4d0a41d 100644
--- a/R/feature_scores.R
+++ b/R/feature_scores.R
@@ -1,4 +1,5 @@
 #' @import AdjacencyScore
+#' @import pheatmap
 #'
 NULL
 
@@ -9,18 +10,26 @@ NULL
 #' @param adj_score_output output of any of the AdjScore functions
 #' - a matrix where each row contains the features in a pair and their
 #' Adjacency Score and q values
+#' @param scaling scaling factor applied in the visualization of q-values.
+#' The q-value are transformed according to -log10(scaling + q-value)
+#' @param style plotting style for the heatmap, to choose between "heatmap"
+#' (default) and "pheatmap"
 #'
 #' @export
 #'
-AdjScoreHeatmap <- function(adj_score_output) {
+AdjScoreHeatmap <- function(adj_score_output, scaling = 1e-10, style = "heatmap") {
   heatmap_matrix <- matrix(rep(0,length(unique(adj_score_output$f))*length(unique(adj_score_output$g))), ncol=length(unique(adj_score_output$g)))
   row.names(heatmap_matrix) <- unique(adj_score_output$f)[order(unique(adj_score_output$f))]
   colnames(heatmap_matrix) <- unique(adj_score_output$g)[order(unique(adj_score_output$g))]
   for (i in 1:nrow(adj_score_output)) {
-    heatmap_matrix[adj_score_output[i,"f"],adj_score_output[i,"g"]] <- log10(adj_score_output[i,"q"]+1e-15)
-    heatmap_matrix[adj_score_output[i,"g"],adj_score_output[i,"f"]] <- log10(adj_score_output[i,"q"]+1e-15)
+    heatmap_matrix[adj_score_output[i,"f"],adj_score_output[i,"g"]] <- -log10(adj_score_output[i,"q"]+scaling)
+    heatmap_matrix[adj_score_output[i,"g"],adj_score_output[i,"f"]] <- -log10(adj_score_output[i,"q"]+scaling)
+  }
+  if (style=="heatmap") {
+    heatmap(heatmap_matrix, margins=c(10,10), symm=T)
+  } else if (style=="pheatmap") {
+    pheatmap(heatmap_matrix, main=paste0("-log10(",as.character(scaling)," + q-value)"))
   }
-  heatmap(heatmap_matrix, margins=c(10,10), symm=T)
 }