Skip to content

Changing annotation bar width with scaling factor. #97

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
PStaus wants to merge 6 commits into
base: master
Choose a base branch
from
Open

Changing annotation bar width with scaling factor. #97

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
6 commits
Select commit Hold shift + click to select a range
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
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion DESCRIPTION
View file
Open in desktop
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 <rkolde@gmail.com>
Expand Down
6 changes: 5 additions & 1 deletion NEWS
View file
Open in desktop
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
View file
Open in desktop
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