Merge pull request #94 from LieberInstitute/layer_stat_cor_plot_original_colors

Add color_scale flexibility to layer_stat_cor_plot()

Author: lcolladotor

R/layer_stat_cor_plot.R

@@ -16,9 +16,10 @@
 #' the color scale (should be between 0 and 1).
 #' @param color_min A `numeric(1)` specifying the lowest correlation value for
 #' the color scale (should be between 0 and -1).
-#' @param color_scale A `character(3)` vector specifying the color scale for the
-#' fill of the heatmap. The first value is used for `color_min`, the second one
-#' for zero, and the third for `color_max`.
+#' @param color_scale A `character` vector with three or more values specifying 
+#' the color scale for the fill of the heatmap. The first value is used for 
+#' `color_min`, the middle for zero, and the last for `color_max`. If an even 
+#' number of colors are supplied, the last color is dropped to center zero.
 #' @param query_colors named `character` vector of colors, Adds colors to query
 #' row annotations.
 #' @param reference_colors named `character` vector of colors, Adds colors to
@@ -64,7 +65,7 @@
 #' ## Default plot with no annotations and defaults for ComplexHeatmap()
 #' layer_stat_cor_plot(cor_stats_layer)
 #'
-#' ## add colors
+#' ## add Annotation colors
 #' ## add libd_layer_colors to reference Human Pilot layers
 #' layer_stat_cor_plot(cor_stats_layer, reference_colors = libd_layer_colors)
 #'
@@ -87,31 +88,55 @@
 #'     confidence_threshold = .55
 #' )
 #' layer_stat_cor_plot(cor_stats_layer, annotation = annotation_df)
-#'
+#' 
+#' ## change fill color scale
+#' layer_stat_cor_plot(cor_stats_layer, 
+#'                     color_scale = RColorBrewer::brewer.pal(2, "PiYG"))
+#' 
 #' ## All together
 #' layer_stat_cor_plot(
-#'     cor_stats_layer,
+#'     cor_stats_layer, 
+#'     color_scale = RColorBrewer::brewer.pal(5, "PiYG"),
 #'     query_colors = cluster_colors,
 #'     reference_colors = libd_layer_colors,
 #'     annotation = annotation_df,
 #'     cluster_rows = FALSE,
 #'     cluster_columns = FALSE
 #' )
 #'
-layer_stat_cor_plot <- function(cor_stats_layer,
-    color_max = max(cor_stats_layer),
-    color_min = min(cor_stats_layer),
-    color_scale = c("#762A83", "#F7F7F7", "#1B7837"),
-    query_colors = NULL,
-    reference_colors = NULL,
-    annotation = NULL,
-    ...) {
+layer_stat_cor_plot <- function(
+        cor_stats_layer,
+        color_max = max(cor_stats_layer),
+        color_min = min(cor_stats_layer),
+        color_scale = RColorBrewer::brewer.pal(7, "PRGn"),
+        query_colors = NULL,
+        reference_colors = NULL,
+        annotation = NULL,
+        ...) {
     ## define color pallet
     stopifnot(color_min < color_max)
     stopifnot(color_min < 0)
-    stopifnot(length(color_scale) == 3)
-    my.col <- circlize::colorRamp2(c(color_min, 0, color_max), color_scale)
-
+    stopifnot(length(color_scale) >= 3)
+    # my.col <- circlize::colorRamp2(c(color_min, 0, color_max), color_scale)
+    
+    # create a sequence from color_min to color max centered around 0
+    n.col <- length(color_scale)
+    zero_center_seq <- unique(c(seq(color_min, 0, length.out = ceiling(n.col/2)),
+                                seq(0, color_max, length.out = ceiling(n.col/2))))
+    
+    if(!length(color_scale) == length(zero_center_seq)){
+      warning(sprintf("Using %d/%d colors to center zero, dropping %s",
+                      length(zero_center_seq),
+                      n.col,
+                      color_scale[n.col]), call. = FALSE)
+      color_scale <- color_scale[seq(length(zero_center_seq))]
+    }
+    
+    my.col <- circlize::colorRamp2(
+      breaks = zero_center_seq,
+      colors = color_scale
+    )
+    
     # ## query annotations on row
     if (!is.null(query_colors)) {
         stopifnot(all(rownames(cor_stats_layer) %in% names(query_colors)))