add stat argument in frequencyHeatmap()

jokergoo · Mar 24, 2021 · 49e4fa6 · 49e4fa6
1 parent c6a77a8
commit 49e4fa6
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Showing 9 changed files with 42 additions and 36 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: ComplexHeatmap
 Type: Package
 Title: Make Complex Heatmaps
-Version: 2.7.9.1003
+Version: 2.7.9.1004
 Date: 2021-3-24
 Author: Zuguang Gu
 Maintainer: Zuguang Gu <[email protected]>

diff --git a/R/00_S4_generic_methods.R b/R/00_S4_generic_methods.R
@@ -1,32 +1,32 @@
-setGeneric('re_size', function(object, ...) standardGeneric('re_size'))
-setGeneric('get_legend_param_list', function(object, ...) standardGeneric('get_legend_param_list'))
+setGeneric('column_order', function(object, ...) standardGeneric('column_order'))
+setGeneric('annotation_legend_size', function(object, ...) standardGeneric('annotation_legend_size'))
+setGeneric('make_layout', function(object, ...) standardGeneric('make_layout'))
+setGeneric('draw_annotation', function(object, ...) standardGeneric('draw_annotation'))
 setGeneric('get_color_mapping_list', function(object, ...) standardGeneric('get_color_mapping_list'))
-setGeneric('prepare', function(object, ...) standardGeneric('prepare'))
-setGeneric('draw_annotation_legend', function(object, ...) standardGeneric('draw_annotation_legend'))
+setGeneric('re_size', function(object, ...) standardGeneric('re_size'))
 setGeneric('draw', function(object, ...) standardGeneric('draw'))
-setGeneric('draw_heatmap_list', function(object, ...) standardGeneric('draw_heatmap_list'))
-setGeneric('draw_title', function(object, ...) standardGeneric('draw_title'))
-setGeneric('add_heatmap', function(object, ...) standardGeneric('add_heatmap'))
-setGeneric('make_layout', function(object, ...) standardGeneric('make_layout'))
-setGeneric('map_to_colors', function(object, ...) standardGeneric('map_to_colors'))
-setGeneric('component_width', function(object, ...) standardGeneric('component_width'))
-setGeneric('column_order', function(object, ...) standardGeneric('column_order'))
-setGeneric('adjust_heatmap_list', function(object, ...) standardGeneric('adjust_heatmap_list'))
-setGeneric('make_column_cluster', function(object, ...) standardGeneric('make_column_cluster'))
 setGeneric('color_mapping_legend', function(object, ...) standardGeneric('color_mapping_legend'))
-setGeneric('draw_heatmap_legend', function(object, ...) standardGeneric('draw_heatmap_legend'))
-setGeneric('draw_dend', function(object, ...) standardGeneric('draw_dend'))
-setGeneric('row_dend', function(object, ...) standardGeneric('row_dend'))
-setGeneric('heatmap_legend_size', function(object, ...) standardGeneric('heatmap_legend_size'))
+setGeneric('draw_heatmap_list', function(object, ...) standardGeneric('draw_heatmap_list'))
 setGeneric('row_order', function(object, ...) standardGeneric('row_order'))
-setGeneric('component_height', function(object, ...) standardGeneric('component_height'))
 setGeneric('draw_dimnames', function(object, ...) standardGeneric('draw_dimnames'))
-setGeneric('make_row_cluster', function(object, ...) standardGeneric('make_row_cluster'))
+setGeneric('row_dend', function(object, ...) standardGeneric('row_dend'))
+setGeneric('column_dend', function(object, ...) standardGeneric('column_dend'))
+setGeneric('set_component_width', function(object, ...) standardGeneric('set_component_width'))
 setGeneric('set_component_height', function(object, ...) standardGeneric('set_component_height'))
-setGeneric('attach_annotation', function(object, ...) standardGeneric('attach_annotation'))
-setGeneric('annotation_legend_size', function(object, ...) standardGeneric('annotation_legend_size'))
-setGeneric('draw_annotation', function(object, ...) standardGeneric('draw_annotation'))
+setGeneric('make_column_cluster', function(object, ...) standardGeneric('make_column_cluster'))
+setGeneric('draw_title', function(object, ...) standardGeneric('draw_title'))
 setGeneric('draw_heatmap_body', function(object, ...) standardGeneric('draw_heatmap_body'))
-setGeneric('set_component_width', function(object, ...) standardGeneric('set_component_width'))
-setGeneric('column_dend', function(object, ...) standardGeneric('column_dend'))
 setGeneric('copy_all', function(object, ...) standardGeneric('copy_all'))
+setGeneric('make_row_cluster', function(object, ...) standardGeneric('make_row_cluster'))
+setGeneric('draw_annotation_legend', function(object, ...) standardGeneric('draw_annotation_legend'))
+setGeneric('adjust_heatmap_list', function(object, ...) standardGeneric('adjust_heatmap_list'))
+setGeneric('component_width', function(object, ...) standardGeneric('component_width'))
+setGeneric('component_height', function(object, ...) standardGeneric('component_height'))
+setGeneric('get_legend_param_list', function(object, ...) standardGeneric('get_legend_param_list'))
+setGeneric('heatmap_legend_size', function(object, ...) standardGeneric('heatmap_legend_size'))
+setGeneric('draw_dend', function(object, ...) standardGeneric('draw_dend'))
+setGeneric('attach_annotation', function(object, ...) standardGeneric('attach_annotation'))
+setGeneric('map_to_colors', function(object, ...) standardGeneric('map_to_colors'))
+setGeneric('add_heatmap', function(object, ...) standardGeneric('add_heatmap'))
+setGeneric('draw_heatmap_legend', function(object, ...) standardGeneric('draw_heatmap_legend'))
+setGeneric('prepare', function(object, ...) standardGeneric('prepare'))
diff --git a/R/densityHeatmap.R b/R/densityHeatmap.R
@@ -349,7 +349,8 @@ ks_dist_1 = function(data) {
 #
 # == param
 # -data A matrix or a list. If it is a matrix, density is calculated by columns.
-# -breaks Pass to `graphics::hist`.
+# -breaks Pass to `graphics::hist`. Please only set equal bin size.
+# -stat Statistic to use.
 # -col A vector of colors that density values are mapped to.
 # -color_space The color space in which colors are interpolated. Pass to `circlize::colorRamp2`.
 # -ylab Label on y-axis.
@@ -470,7 +471,7 @@ frequencyHeatmap = function(data,
 
 
 	if(use_3d) {
-		ht = Heatmap3D(mat, col = col, name = "frequency", 
+		ht = Heatmap3D(mat, col = col, name = stat, 
 			column_title = title,
 			column_title_gp = title_gp,
 			cluster_rows = FALSE, 
@@ -487,7 +488,7 @@ frequencyHeatmap = function(data,
 			...
 		)
 	} else {
-		ht = Heatmap(mat, col = col, name = "frequency", 
+		ht = Heatmap(mat, col = col, name = stat, 
 			column_title = title,
 			column_title_gp = title_gp,
 			cluster_rows = FALSE, 
@@ -520,8 +521,9 @@ frequencyHeatmap = function(data,
 			grid.text(ylab, x = grobHeight(textGrob(ylab, gp = ylab_gp)), rot = 90)
 		}, slice = 1)
 
-		decorate_heatmap_body(paste0("frequency_", random_str), {
+		decorate_heatmap_body(paste0(stat, "_", random_str), {
 			pushViewport(viewport(yscale = c(min_x, max_x), clip = FALSE))
+			grid.segments(0, 0, 0, 1)
 			grid.yaxis(gp = tick_label_gp)
 			upViewport()
 		}, column_slice = 1)

diff --git a/man/Heatmap3D.Rd b/man/Heatmap3D.Rd
@@ -15,6 +15,7 @@ Heatmap3D(matrix,
     bar_max_length = unit(1, "cm"),
     bar_angle = 60,
 
+    row_names_side = "left",
     show_row_dend = FALSE,
     show_column_dend = FALSE)
 }
@@ -26,6 +27,7 @@ Heatmap3D(matrix,
   \item{bar_rel_height}{A factor between 0 and 1.}
   \item{bar_max_length}{Maximal length of bars. Value should be in absolute unit.}
   \item{bar_angle}{Angle for the projection.}
+  \item{row_names_side}{Row names are by default put on the left side of the heatmap.}
   \item{show_row_dend}{By default the dendrogram is not drawn.}
   \item{show_column_dend}{By default the dendrogram is not drawn.}
 

diff --git a/man/copy_all-dispatch.Rd b/man/copy_all-dispatch.Rd
@@ -10,8 +10,8 @@ Method dispatch page for \code{copy_all}.
 \code{copy_all} can be dispatched on following classes:
 
 \itemize{
-\item \code{\link{copy_all,AnnotationFunction-method}}, \code{\link{AnnotationFunction-class}} class method
 \item \code{\link{copy_all,SingleAnnotation-method}}, \code{\link{SingleAnnotation-class}} class method
+\item \code{\link{copy_all,AnnotationFunction-method}}, \code{\link{AnnotationFunction-class}} class method
 }
 }
 \examples{

diff --git a/man/draw-dispatch.Rd b/man/draw-dispatch.Rd
@@ -11,10 +11,10 @@ Method dispatch page for \code{draw}.
 
 \itemize{
 \item \code{\link{draw,Heatmap-method}}, \code{\link{Heatmap-class}} class method
-\item \code{\link{draw,SingleAnnotation-method}}, \code{\link{SingleAnnotation-class}} class method
-\item \code{\link{draw,AnnotationFunction-method}}, \code{\link{AnnotationFunction-class}} class method
 \item \code{\link{draw,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method
 \item \code{\link{draw,Legends-method}}, \code{\link{Legends-class}} class method
+\item \code{\link{draw,AnnotationFunction-method}}, \code{\link{AnnotationFunction-class}} class method
+\item \code{\link{draw,SingleAnnotation-method}}, \code{\link{SingleAnnotation-class}} class method
 \item \code{\link{draw,HeatmapAnnotation-method}}, \code{\link{HeatmapAnnotation-class}} class method
 }
 }

diff --git a/man/frequencyHeatmap.Rd b/man/frequencyHeatmap.Rd
@@ -9,6 +9,7 @@ Visualize Frequency Distribution by Heatmap
 \usage{
 frequencyHeatmap(data,
     breaks = "Sturges",
+    stat = c("count", "density", "proportion"),
 
     col = brewer.pal(9, "Blues"),
     color_space = "LAB",
@@ -36,7 +37,8 @@ frequencyHeatmap(data,
 \arguments{
 
   \item{data}{A matrix or a list. If it is a matrix, density is calculated by columns.}
-  \item{breaks}{Pass to \code{\link[graphics]{hist}}.}
+  \item{breaks}{Pass to \code{\link[graphics]{hist}}. Please only set equal bin size.}
+  \item{stat}{Statistic to use.}
   \item{col}{A vector of colors that density values are mapped to.}
   \item{color_space}{The color space in which colors are interpolated. Pass to \code{\link[circlize]{colorRamp2}}.}
   \item{ylab}{Label on y-axis.}

diff --git a/man/row_dend-dispatch.Rd b/man/row_dend-dispatch.Rd
@@ -10,8 +10,8 @@ Method dispatch page for \code{row_dend}.
 \code{row_dend} can be dispatched on following classes:
 
 \itemize{
-\item \code{\link{row_dend,Heatmap-method}}, \code{\link{Heatmap-class}} class method
 \item \code{\link{row_dend,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method
+\item \code{\link{row_dend,Heatmap-method}}, \code{\link{Heatmap-class}} class method
 }
 }
 \examples{

diff --git a/man/show-dispatch.Rd b/man/show-dispatch.Rd
@@ -11,11 +11,11 @@ Method dispatch page for \code{show}.
 
 \itemize{
 \item \code{\link{show,AnnotationFunction-method}}, \code{\link{AnnotationFunction-class}} class method
-\item \code{\link{show,SingleAnnotation-method}}, \code{\link{SingleAnnotation-class}} class method
 \item \code{\link{show,Heatmap-method}}, \code{\link{Heatmap-class}} class method
+\item \code{\link{show,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method
 \item \code{\link{show,HeatmapAnnotation-method}}, \code{\link{HeatmapAnnotation-class}} class method
 \item \code{\link{show,ColorMapping-method}}, \code{\link{ColorMapping-class}} class method
-\item \code{\link{show,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method
+\item \code{\link{show,SingleAnnotation-method}}, \code{\link{SingleAnnotation-class}} class method
 }
 }
 \examples{