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Changing annotation bar width with scaling factor. #97

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Changing annotation bar width with scaling factor. #97

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dd711f1
add pheadmap.r file for scaling annotation bar
PStaus Jun 9, 2023
baa65b7
Update pheatmap.r
PStaus Jun 9, 2023
40340ff
Delete pheatmap.r
PStaus Jun 9, 2023
034f189
Update NEWS
PStaus Jun 9, 2023
966d683
Update DESCRIPTION
PStaus Jun 9, 2023
fb86c2e
Update pheatmap.r
PStaus Jun 9, 2023
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2 changes: 1 addition & 1 deletion DESCRIPTION
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
Package: pheatmap
Type: Package
Title: Pretty Heatmaps
Version: 1.0.12
Version: 1.0.13
Date: 2018-12-26
Author: Raivo Kolde
Maintainer: Raivo Kolde <[email protected]>
Expand Down
6 changes: 5 additions & 1 deletion NEWS
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Original file line number Diff line number Diff line change
@@ -1,3 +1,7 @@
Version 1.0.13
------------------------------------------------------------------------------
* New option to change width of annotation bar

Version 1.0.12
-------------------------------------------------------------------------------
* New option angle_col that allows to change the orientation of column labels
Expand Down Expand Up @@ -126,4 +130,4 @@ legend (drop_levels parameter).
* Changed the order how the rows are drawn when rows are not clustered. Before
it started from the bottom, now from the top.
* Changed legend positioning according to the presence of column names
* The function now returns invisibly all the clusterings that it performed.
* The function now returns invisibly all the clusterings that it performed.
37 changes: 19 additions & 18 deletions R/pheatmap.r
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
lo = function(rown, coln, nrow, ncol, cellheight = NA, cellwidth = NA, treeheight_col, treeheight_row, legend, annotation_row, annotation_col, annotation_colors, annotation_legend, annotation_names_row, annotation_names_col, main, fontsize, fontsize_row , fontsize_col, angle_col, gaps_row, gaps_col, ...){
lo = function(rown, coln, nrow, ncol, cellheight = NA, cellwidth = NA, treeheight_col, treeheight_row, legend, annotation_row, annotation_col, annotation_colors, annotation_legend, annotation_names_row, annotation_names_col, annotation_scale, main, fontsize, fontsize_row , fontsize_col, angle_col, gaps_row, gaps_col, ...){
# Get height of colnames and length of rownames
if(!is.null(coln[1]) | (!is.na2(annotation_row) & annotation_names_row)){
if(!is.null(coln[1])){
Expand Down Expand Up @@ -60,7 +60,7 @@ lo = function(rown, coln, nrow, ncol, cellheight = NA, cellwidth = NA, treeheigh

if(!is.na2(annotation_col)){
# Column annotation height
annot_col_height = ncol(annotation_col) * (textheight + unit(2, "bigpts")) + unit(2, "bigpts")
annot_col_height = ncol(annotation_col) * (textheight * annotation_scale + unit(2, "bigpts")) + unit(2, "bigpts")

# Width of the correponding legend
t = c(as.vector(as.matrix(annotation_col)), colnames(annotation_col))
Expand All @@ -77,7 +77,7 @@ lo = function(rown, coln, nrow, ncol, cellheight = NA, cellwidth = NA, treeheigh
# Row annotations
if(!is.na2(annotation_row)){
# Row annotation width
annot_row_width = ncol(annotation_row) * (textheight + unit(2, "bigpts")) + unit(2, "bigpts")
annot_row_width = ncol(annotation_row) * (textheight * annotation_scale + unit(2, "bigpts")) + unit(2, "bigpts")

# Width of the correponding legend
t = c(as.vector(as.matrix(annotation_row)), colnames(annotation_row))
Expand Down Expand Up @@ -279,7 +279,7 @@ convert_annotations = function(annotation, annotation_colors){
return(as.matrix(new))
}

draw_annotations = function(converted_annotations, border_color, gaps, fontsize, horizontal){
draw_annotations = function(converted_annotations, border_color, gaps, fontsize, horizontal, annotation_scale){
n = ncol(converted_annotations)
m = nrow(converted_annotations)

Expand All @@ -288,31 +288,31 @@ draw_annotations = function(converted_annotations, border_color, gaps, fontsize,
x = coord_x$coord - 0.5 * coord_x$size

# y = cumsum(rep(fontsize, n)) - 4 + cumsum(rep(2, n))
y = cumsum(rep(fontsize, n)) + cumsum(rep(2, n)) - fontsize / 2 + 1
y = cumsum(rep(fontsize * annotation_scale, n)) + cumsum(rep(2, n)) - (fontsize * annotation_scale) / 2 + 1
y = unit(y, "bigpts")

if(horizontal){
coord = expand.grid(x = x, y = y)
res = rectGrob(x = coord$x, y = coord$y, width = coord_x$size, height = unit(fontsize, "bigpts"), gp = gpar(fill = converted_annotations, col = border_color))
res = rectGrob(x = coord$x, y = coord$y, width = coord_x$size, height = unit(fontsize * annotation_scale, "bigpts"), gp = gpar(fill = converted_annotations, col = border_color))
}
else{
a = x
x = unit(1, "npc") - y
y = unit(1, "npc") - a

coord = expand.grid(y = y, x = x)
res = rectGrob(x = coord$x, y = coord$y, width = unit(fontsize, "bigpts"), height = coord_x$size, gp = gpar(fill = converted_annotations, col = border_color))
res = rectGrob(x = coord$x, y = coord$y, width = unit(fontsize * annotation_scale, "bigpts"), height = coord_x$size, gp = gpar(fill = converted_annotations, col = border_color))
}

return(res)
}

draw_annotation_names = function(annotations, fontsize, horizontal, hjust_col, vjust_col, angle_col){
draw_annotation_names = function(annotations, fontsize, horizontal, hjust_col, vjust_col, angle_col, annotation_scale){
n = ncol(annotations)

x = unit(3, "bigpts")

y = cumsum(rep(fontsize, n)) + cumsum(rep(2, n)) - fontsize / 2 + 1
y = cumsum(rep(fontsize * annotation_scale, n)) + cumsum(rep(2, n)) - (fontsize * annotation_scale) / 2 + 1
y = unit(y, "bigpts")

if(horizontal){
Expand Down Expand Up @@ -378,9 +378,9 @@ vplayout = function(x, y){
return(viewport(layout.pos.row = x, layout.pos.col = y))
}

heatmap_motor = function(matrix, border_color, cellwidth, cellheight, tree_col, tree_row, treeheight_col, treeheight_row, filename, width, height, breaks, color, legend, annotation_row, annotation_col, annotation_colors, annotation_legend, annotation_names_row, annotation_names_col, main, fontsize, fontsize_row, fontsize_col, hjust_col, vjust_col, angle_col, fmat, fontsize_number, number_color, gaps_col, gaps_row, labels_row, labels_col, ...){
heatmap_motor = function(matrix, border_color, cellwidth, cellheight, tree_col, tree_row, treeheight_col, treeheight_row, filename, width, height, breaks, color, legend, annotation_row, annotation_col, annotation_colors, annotation_legend, annotation_names_row, annotation_names_col, annotation_scale, main, fontsize, fontsize_row, fontsize_col, hjust_col, vjust_col, angle_col, fmat, fontsize_number, number_color, gaps_col, gaps_row, labels_row, labels_col, ...){
# Set layout
lo = lo(coln = labels_col, rown = labels_row, nrow = nrow(matrix), ncol = ncol(matrix), cellwidth = cellwidth, cellheight = cellheight, treeheight_col = treeheight_col, treeheight_row = treeheight_row, legend = legend, annotation_col = annotation_col, annotation_row = annotation_row, annotation_colors = annotation_colors, annotation_legend = annotation_legend, annotation_names_row = annotation_names_row, annotation_names_col = annotation_names_col, main = main, fontsize = fontsize, fontsize_row = fontsize_row, fontsize_col = fontsize_col, angle_col = angle_col, gaps_row = gaps_row, gaps_col = gaps_col, ...)
lo = lo(coln = labels_col, rown = labels_row, nrow = nrow(matrix), ncol = ncol(matrix), cellwidth = cellwidth, cellheight = cellheight, treeheight_col = treeheight_col, treeheight_row = treeheight_row, legend = legend, annotation_col = annotation_col, annotation_row = annotation_row, annotation_colors = annotation_colors, annotation_legend = annotation_legend, annotation_names_row = annotation_names_row, annotation_names_col = annotation_names_col, annotation_scale = annotation_scale, main = main, fontsize = fontsize, fontsize_row = fontsize_row, fontsize_col = fontsize_col, angle_col = angle_col, gaps_row = gaps_row, gaps_col = gaps_col, ...)

res = lo$gt
mindim = lo$mindim
Expand Down Expand Up @@ -413,7 +413,7 @@ heatmap_motor = function(matrix, border_color, cellwidth, cellheight, tree_col,
# gt = heatmap_motor(matrix, cellwidth = cellwidth, cellheight = cellheight, border_color = border_color, tree_col = tree_col, tree_row = tree_row, treeheight_col = treeheight_col, treeheight_row = treeheight_row, breaks = breaks, color = color, legend = legend, annotation_col = annotation_col, annotation_row = annotation_row, annotation_colors = annotation_colors, annotation_legend = annotation_legend, filename = NA, main = main, fontsize = fontsize, fontsize_row = fontsize_row, fontsize_col = fontsize_col, fmat = fmat, fontsize_number = fontsize_number, number_color = number_color, labels_row = labels_row, labels_col = labels_col, gaps_col = gaps_col, gaps_row = gaps_row, ...)

f(filename, height = height, width = width)
gt = heatmap_motor(matrix, cellwidth = cellwidth, cellheight = cellheight, border_color = border_color, tree_col = tree_col, tree_row = tree_row, treeheight_col = treeheight_col, treeheight_row = treeheight_row, breaks = breaks, color = color, legend = legend, annotation_col = annotation_col, annotation_row = annotation_row, annotation_colors = annotation_colors, annotation_legend = annotation_legend, annotation_names_row = annotation_names_row, annotation_names_col = annotation_names_col, filename = NA, main = main, fontsize = fontsize, fontsize_row = fontsize_row, fontsize_col = fontsize_col, hjust_col = hjust_col, vjust_col = vjust_col, angle_col = angle_col, fmat = fmat, fontsize_number = fontsize_number, number_color = number_color, labels_row = labels_row, labels_col = labels_col, gaps_col = gaps_col, gaps_row = gaps_row, ...)
gt = heatmap_motor(matrix, cellwidth = cellwidth, cellheight = cellheight, border_color = border_color, tree_col = tree_col, tree_row = tree_row, treeheight_col = treeheight_col, treeheight_row = treeheight_row, breaks = breaks, color = color, legend = legend, annotation_col = annotation_col, annotation_row = annotation_row, annotation_colors = annotation_colors, annotation_legend = annotation_legend, annotation_names_row = annotation_names_row, annotation_names_col = annotation_names_col, annotation_scale = annotation_scale , filename = NA, main = main, fontsize = fontsize, fontsize_row = fontsize_row, fontsize_col = fontsize_col, hjust_col = hjust_col, vjust_col = vjust_col, angle_col = angle_col, fmat = fmat, fontsize_number = fontsize_number, number_color = number_color, labels_row = labels_row, labels_col = labels_col, gaps_col = gaps_col, gaps_row = gaps_row, ...)
grid.draw(gt)
dev.off()

Expand Down Expand Up @@ -463,12 +463,12 @@ heatmap_motor = function(matrix, border_color, cellwidth, cellheight, tree_col,
if(!is.na2(annotation_col)){
# Draw tracks
converted_annotation = convert_annotations(annotation_col, annotation_colors)
elem = draw_annotations(converted_annotation, border_color, gaps_col, fontsize, horizontal = T)
elem = draw_annotations(converted_annotation, border_color, gaps_col, fontsize, horizontal = T, annotation_scale)
res = gtable_add_grob(res, elem, t = 3, l = 3, clip = "off", name = "col_annotation")

# Draw names
if(annotation_names_col){
elem = draw_annotation_names(annotation_col, fontsize, horizontal = T)
elem = draw_annotation_names(annotation_col, fontsize, horizontal = T, annotation_scale = annotation_scale)
res = gtable_add_grob(res, elem, t = 3, l = 4, clip = "off", name = "col_annotation_names")
}
}
Expand All @@ -477,12 +477,12 @@ heatmap_motor = function(matrix, border_color, cellwidth, cellheight, tree_col,
if(!is.na2(annotation_row)){
# Draw tracks
converted_annotation = convert_annotations(annotation_row, annotation_colors)
elem = draw_annotations(converted_annotation, border_color, gaps_row, fontsize, horizontal = F)
elem = draw_annotations(converted_annotation, border_color, gaps_row, fontsize, horizontal = F, annotation_scale)
res = gtable_add_grob(res, elem, t = 4, l = 2, clip = "off", name = "row_annotation")

# Draw names
if(annotation_names_row){
elem = draw_annotation_names(annotation_row, fontsize, horizontal = F, hjust_col = hjust_col, vjust_col = vjust_col, angle_col = angle_col)
elem = draw_annotation_names(annotation_row, fontsize, horizontal = F, hjust_col = hjust_col, vjust_col = vjust_col, angle_col = angle_col, annotation_scale = annotation_scale)
res = gtable_add_grob(res, elem, t = 5, l = 2, clip = "off", name = "row_annotation_names")
}
}
Expand Down Expand Up @@ -740,6 +740,7 @@ identity2 = function(x, ...){
#' tracks should be drawn.
#' @param annotation_names_col boolean value showing if the names for column annotation
#' tracks should be drawn.
#' @param annotation_scale Scale factor for the annotation bar. (Default: 1).
#' @param drop_levels logical to determine if unused levels are also shown in
#' the legend
#' @param show_rownames boolean specifying if column names are be shown.
Expand Down Expand Up @@ -882,7 +883,7 @@ identity2 = function(x, ...){
#' }
#'
#' @export
pheatmap = function(mat, color = colorRampPalette(rev(brewer.pal(n = 7, name = "RdYlBu")))(100), kmeans_k = NA, breaks = NA, border_color = "grey60", cellwidth = NA, cellheight = NA, scale = "none", cluster_rows = TRUE, cluster_cols = TRUE, clustering_distance_rows = "euclidean", clustering_distance_cols = "euclidean", clustering_method = "complete", clustering_callback = identity2, cutree_rows = NA, cutree_cols = NA, treeheight_row = ifelse((class(cluster_rows) == "hclust") || cluster_rows, 50, 0), treeheight_col = ifelse((class(cluster_cols) == "hclust") || cluster_cols, 50, 0), legend = TRUE, legend_breaks = NA, legend_labels = NA, annotation_row = NA, annotation_col = NA, annotation = NA, annotation_colors = NA, annotation_legend = TRUE, annotation_names_row = TRUE, annotation_names_col = TRUE, drop_levels = TRUE, show_rownames = T, show_colnames = T, main = NA, fontsize = 10, fontsize_row = fontsize, fontsize_col = fontsize, angle_col = c("270", "0", "45", "90", "315"), display_numbers = F, number_format = "%.2f", number_color = "grey30", fontsize_number = 0.8 * fontsize, gaps_row = NULL, gaps_col = NULL, labels_row = NULL, labels_col = NULL, filename = NA, width = NA, height = NA, silent = FALSE, na_col = "#DDDDDD", ...){
pheatmap = function(mat, color = colorRampPalette(rev(brewer.pal(n = 7, name = "RdYlBu")))(100), kmeans_k = NA, breaks = NA, border_color = "grey60", cellwidth = NA, cellheight = NA, scale = "none", cluster_rows = TRUE, cluster_cols = TRUE, clustering_distance_rows = "euclidean", clustering_distance_cols = "euclidean", clustering_method = "complete", clustering_callback = identity2, cutree_rows = NA, cutree_cols = NA, treeheight_row = ifelse((class(cluster_rows) == "hclust") || cluster_rows, 50, 0), treeheight_col = ifelse((class(cluster_cols) == "hclust") || cluster_cols, 50, 0), legend = TRUE, legend_breaks = NA, legend_labels = NA, annotation_row = NA, annotation_col = NA, annotation = NA, annotation_colors = NA, annotation_legend = TRUE, annotation_names_row = TRUE, annotation_names_col = TRUE, annotation_scale = 1, drop_levels = TRUE, show_rownames = T, show_colnames = T, main = NA, fontsize = 10, fontsize_row = fontsize, fontsize_col = fontsize, angle_col = c("270", "0", "45", "90", "315"), display_numbers = F, number_format = "%.2f", number_color = "grey30", fontsize_number = 0.8 * fontsize, gaps_row = NULL, gaps_col = NULL, labels_row = NULL, labels_col = NULL, filename = NA, width = NA, height = NA, silent = FALSE, na_col = "#DDDDDD", ...){

# Set labels
if(is.null(labels_row)){
Expand Down Expand Up @@ -1090,7 +1091,7 @@ pheatmap = function(mat, color = colorRampPalette(rev(brewer.pal(n = 7, name = "

# Draw heatmap
pdf(file = NULL)
gt = heatmap_motor(mat, border_color = border_color, cellwidth = cellwidth, cellheight = cellheight, treeheight_col = treeheight_col, treeheight_row = treeheight_row, tree_col = tree_col, tree_row = tree_row, filename = filename, width = width, height = height, breaks = breaks, color = color, legend = legend, annotation_row = annotation_row, annotation_col = annotation_col, annotation_colors = annotation_colors, annotation_legend = annotation_legend, annotation_names_row = annotation_names_row, annotation_names_col = annotation_names_col, main = main, fontsize = fontsize, fontsize_row = fontsize_row, fontsize_col = fontsize_col, hjust_col = hjust_col, vjust_col = vjust_col, angle_col = angle_col, fmat = fmat, fontsize_number = fontsize_number, number_color = number_color, gaps_row = gaps_row, gaps_col = gaps_col, labels_row = labels_row, labels_col = labels_col, ...)
gt = heatmap_motor(mat, border_color = border_color, cellwidth = cellwidth, cellheight = cellheight, treeheight_col = treeheight_col, treeheight_row = treeheight_row, tree_col = tree_col, tree_row = tree_row, filename = filename, width = width, height = height, breaks = breaks, color = color, legend = legend, annotation_row = annotation_row, annotation_col = annotation_col, annotation_colors = annotation_colors, annotation_legend = annotation_legend, annotation_names_row = annotation_names_row, annotation_names_col = annotation_names_col, annotation_scale = annotation_scale, main = main, fontsize = fontsize, fontsize_row = fontsize_row, fontsize_col = fontsize_col, hjust_col = hjust_col, vjust_col = vjust_col, angle_col = angle_col, fmat = fmat, fontsize_number = fontsize_number, number_color = number_color, gaps_row = gaps_row, gaps_col = gaps_col, labels_row = labels_row, labels_col = labels_col, ...)
dev.off()

if(is.na(filename) & !silent){
Expand Down