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Added support for binary row annotations #3

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Added support for binary row annotations #3

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660ef00
Added support for annotation of the rows with binary categorical vari…
Oct 1, 2013
b9c8804
Update DESCRIPTION and NEWS to reflect row annotation support.
Oct 1, 2013
bcc454d
Updated documentation to reflect row annotation support.
Oct 1, 2013
178b2e0
Rebuilt documentation via roxygen.
Oct 1, 2013
0037b23
Fixed the order of the row annotations so that they match the rows.
Oct 2, 2013
6435529
rbuildignore
Oct 2, 2013
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4 changes: 3 additions & 1 deletion .Rbuildignore
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@@ -1 +1,3 @@
README.md
README.md
^.*\.Rproj$
^\.Rproj\.user$
5 changes: 3 additions & 2 deletions DESCRIPTION
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@@ -1,12 +1,13 @@
Package: pheatmap
Type: Package
Title: Pretty Heatmaps
Version: 0.7.7
Version: 0.7.8
Date: 2013-30-3
Author: Raivo Kolde
Maintainer: Raivo Kolde <[email protected]>
Depends:
R (>= 2.0)
R (>= 2.0),
RColorBrewer
Description: A package for drawing pretty heatmaps in R. The ordinary heatmap
function in R has several drawbacks when it comes to producing publication
quality heatmaps. It is hard to produce pictures with consistent text, cell
Expand Down
1 change: 1 addition & 0 deletions NAMESPACE
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export(pheatmap)
import(grid)
importFrom(RColorBrewer,brewer.pal)
4 changes: 4 additions & 0 deletions NEWS
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@@ -1,3 +1,7 @@
Version 0.7.8
-------------------------------------------------------------------------------
Added support for row annotations (Greg Finak).

Version 0.7.7
-------------------------------------------------------------------------------
Fixed a bug related to calculating space for the column and row names.
Expand Down
172 changes: 150 additions & 22 deletions R/pheatmap.r
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lo = function(rown, coln, nrow, ncol, cellheight = NA, cellwidth = NA, treeheight_col, treeheight_row, legend, annotation, annotation_colors, annotation_legend, main, fontsize, fontsize_row, fontsize_col, ...){
lo = function(rown, coln, nrow, ncol, cellheight = NA, cellwidth = NA, treeheight_col, treeheight_row, legend, annotation, annotation_colors, annotation_legend, main, fontsize, fontsize_row, fontsize_col,row_annotation,row_annotation_legend,row_annotation_colors, ...){
# Get height of colnames and length of rownames
if(!is.null(coln[1])){
longest_coln = which.max(strwidth(coln, units = 'in'))
gp = list(fontsize = fontsize_col, ...)
coln_height = unit(1, "grobheight", textGrob(coln[longest_coln], rot = 90, gp = do.call(gpar, gp))) + unit(5, "bigpts")
if(!is.null(row_annotation)[[1]][1]){
coln<-c(coln,colnames(row_annotation))
longest_coln = which.max(strwidth(coln, units = 'in'))
gp = list(fontsize = fontsize_col, ...)
coln_height = unit(1, "grobheight", textGrob(coln[longest_coln], rot = 90, gp = do.call(gpar, gp))) + unit(5, "bigpts")
}else{
longest_coln = which.max(strwidth(coln, units = 'in'))
gp = list(fontsize = fontsize_col, ...)
coln_height = unit(1, "grobheight", textGrob(coln[longest_coln], rot = 90, gp = do.call(gpar, gp))) + unit(5, "bigpts")
}
}
else{
coln_height = unit(5, "bigpts")
Expand Down Expand Up @@ -54,14 +61,29 @@ lo = function(rown, coln, nrow, ncol, cellheight = NA, cellwidth = NA, treeheigh
annot_height = unit(0, "bigpts")
annot_legend_width = unit(0, "bigpts")
}


# Row annotations
if(!is.na(row_annotation[[1]][1])){
#width of the annoation beside the rows
row_annotation_width = unit(ncol(row_annotation) * (8 + 2) + 2,"bigpts")
#width of the legend
longest_row_annotation = which.max(nchar(as.matrix(row_annotation)))
row_annotation_legend_width = unit(1.2, "grobwidth",textGrob(as.matrix(row_annotation)[longest_row_annotation],gp=gpar(...))) + unit(12,"bigpts")
if(!row_annotation_legend){
row_annotation_legend_width = unit(0,"npc")
}
}else{
row_annotation_width = unit(0,"bigpts")
row_anotation_legend_width= unit(0,"bigpts")
}

# Tree height
treeheight_col = unit(treeheight_col, "bigpts") + unit(5, "bigpts")
treeheight_row = unit(treeheight_row, "bigpts") + unit(5, "bigpts")

# Set cell sizes
if(is.na(cellwidth)){
matwidth = unit(1, "npc") - rown_width - legend_width - treeheight_row - annot_legend_width
matwidth = unit(1, "npc") - rown_width - legend_width - treeheight_row - annot_legend_width - row_annotation_width
}
else{
matwidth = unit(cellwidth * ncol, "bigpts")
Expand All @@ -76,7 +98,10 @@ lo = function(rown, coln, nrow, ncol, cellheight = NA, cellwidth = NA, treeheigh


# Produce layout()
pushViewport(viewport(layout = grid.layout(nrow = 5, ncol = 5, widths = unit.c(treeheight_row, matwidth, rown_width, legend_width, annot_legend_width), heights = unit.c(main_height, treeheight_col, annot_height, matheight, coln_height)), gp = do.call(gpar, gp)))
pushViewport(viewport(layout =
grid.layout(nrow = 5, ncol = 6,
widths = unit.c(treeheight_row, matwidth, row_annotation_width, rown_width, legend_width, annot_legend_width),
heights = unit.c(main_height, treeheight_col, annot_height, matheight, coln_height)), gp = do.call(gpar, gp)))

# Get cell dimensions
pushViewport(vplayout(4, 2))
Expand Down Expand Up @@ -195,6 +220,16 @@ draw_annotations = function(converted_annotations, border_color){
}
}

draw_row_annotations = function(converted_annotations, border_color){
n = ncol(converted_annotations)
m = nrow(converted_annotations)
y = rev((1:m)/m - 1/2/m)
x = cumsum(rep(8, n)) - 4 + cumsum(rep(2, n))
for(i in 1:m){
grid.rect(y = y[i], unit(x[1:n], "bigpts"), height = 1/m, width = unit(8, "bigpts"), gp = gpar(fill = converted_annotations[i, ], col = border_color))
}
}

draw_annotation_legend = function(annotation, annotation_colors, border_color, ...){
y = unit(1, "npc")
text_height = unit(1, "grobheight", textGrob("FGH", gp = gpar(...)))
Expand Down Expand Up @@ -229,14 +264,14 @@ 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, annotation_colors, annotation_legend, main, fontsize, fontsize_row, fontsize_col, fmat, fontsize_number, ...){
heatmap_motor = function(matrix, border_color, cellwidth, cellheight, tree_col, tree_row, treeheight_col, treeheight_row, filename, width, height, breaks, color, legend, annotation, annotation_colors, annotation_legend, main, fontsize, fontsize_row, fontsize_col, fmat, fontsize_number, row_annotation, row_annotation_legend, row_annotation_colors, ...){
grid.newpage()

# Set layout
mindim = lo(coln = colnames(matrix), rown = rownames(matrix), nrow = nrow(matrix), ncol = ncol(matrix), cellwidth = cellwidth, cellheight = cellheight, treeheight_col = treeheight_col, treeheight_row = treeheight_row, legend = legend, annotation = annotation, annotation_colors = annotation_colors, annotation_legend = annotation_legend, main = main, fontsize = fontsize, fontsize_row = fontsize_row, fontsize_col = fontsize_col, ...)
mindim = lo(coln = colnames(matrix), rown = rownames(matrix), nrow = nrow(matrix), ncol = ncol(matrix), cellwidth = cellwidth, cellheight = cellheight, treeheight_col = treeheight_col, treeheight_row = treeheight_row, legend = legend, annotation = annotation, annotation_colors = annotation_colors, annotation_legend = annotation_legend, main = main, fontsize = fontsize, fontsize_row = fontsize_row, fontsize_col = fontsize_col, row_annotation = row_annotation, row_annotation_legend = row_annotation_legend, row_annotation_colors = row_annotation_colors, ...)

if(!is.na(filename)){
pushViewport(vplayout(1:5, 1:5))
pushViewport(vplayout(1:5, 1:6)) #edited

if(is.na(height)){
height = convertHeight(unit(0:1, "npc"), "inches", valueOnly = T)[2]
Expand All @@ -262,7 +297,7 @@ heatmap_motor = function(matrix, border_color, cellwidth, cellheight, tree_col,

# print(sprintf("height:%f width:%f", height, width))
f(filename, height = height, width = width)
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 = annotation, 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, ...)
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 = annotation, 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, row_annotation = row_annotation, row_annotation_legend = row_annotation_legend, ...)
dev.off()
upViewport()
return()
Expand Down Expand Up @@ -307,7 +342,7 @@ heatmap_motor = function(matrix, border_color, cellwidth, cellheight, tree_col,

# Draw rownames
if(length(rownames(matrix)) != 0){
pushViewport(vplayout(4, 3))
pushViewport(vplayout(4, 4)) #edited
pars = list(rownames(matrix), fontsize = fontsize_row, ...)
do.call(draw_rownames, pars)
upViewport()
Expand All @@ -321,13 +356,26 @@ heatmap_motor = function(matrix, border_color, cellwidth, cellheight, tree_col,
upViewport()
}

#Draw row annotation tracks
if(!is.na(row_annotation[[1]][1])){
pushViewport(vplayout(4,3))
converted_row_annotations = convert_annotations(row_annotation, row_annotation_colors)
draw_row_annotations(converted_row_annotations, border_color)
upViewport()
#label the rows
pushViewport(vplayout(5,3))
pars_row_annotations = list(colnames(converted_row_annotations), fontsize = fontsize_col, ...)
do.call(draw_colnames, pars_row_annotations)
upViewport()
}

# Draw annotation legend
if(!is.na(annotation[[1]][1]) & annotation_legend){
if(length(rownames(matrix)) != 0){
pushViewport(vplayout(4:5, 5))
pushViewport(vplayout(4:5, 6)) #edited
}
else{
pushViewport(vplayout(3:5, 5))
pushViewport(vplayout(3:5, 6)) #edited
}
draw_annotation_legend(annotation, annotation_colors, border_color, fontsize = fontsize, ...)
upViewport()
Expand All @@ -337,10 +385,10 @@ heatmap_motor = function(matrix, border_color, cellwidth, cellheight, tree_col,
if(!is.na(legend[1])){
length(colnames(matrix))
if(length(rownames(matrix)) != 0){
pushViewport(vplayout(4:5, 4))
pushViewport(vplayout(4:5, 5)) #edited
}
else{
pushViewport(vplayout(3:5, 4))
pushViewport(vplayout(3:5, 5)) #edited
}
draw_legend(color, breaks, legend, fontsize = fontsize, ...)
upViewport()
Expand Down Expand Up @@ -454,6 +502,69 @@ generate_annotation_colours = function(annotation, annotation_colors, drop){
return(annotation_colors)
}



generate_row_annotation_colours = function(annotation, annotation_colors, drop){
if(is.na(annotation_colors)[[1]][1]){
annotation_colors = list()
}
count = 0
for(i in 1:ncol(annotation)){
if(is.character(annotation[, i]) | is.factor(annotation[, i])){
if (is.factor(annotation[, i]) & !drop){
if(length(levels(annotation[, i]))>2){
stop("Each row annotation category must have no more than two levels.")
}
count = count + length(levels(annotation[, i]))
}
else{
if(length(unique(annotation[, i]))>2){
stop("Each row annotation category must have no more than two levels.")
}
count = count + length(unique(annotation[, i]))
}
}
}

factor_colors = hsv((seq(0, 1, length.out = count + 1)[-1] +
0.2)%%1, 0.7, 0.95)

set.seed(3453)

for(i in 1:ncol(annotation)){
if(!(colnames(annotation)[i] %in% names(annotation_colors))){
if(is.character(annotation[, i]) | is.factor(annotation[, i])){
n = length(unique(annotation[, i]))
if (is.factor(annotation[, i]) & !drop){
n = length(levels(annotation[, i]))
}
ind = sample(1:length(factor_colors), n)
annotation_colors[[colnames(annotation)[i]]] = factor_colors[ind]
l = levels(as.factor(annotation[, i]))
l = l[l %in% unique(annotation[, i])]
if (is.factor(annotation[, i]) & !drop){
l = levels(annotation[, i])
}
names(annotation_colors[[colnames(annotation)[i]]]) = l
factor_colors = factor_colors[-ind]
}
else{
r = runif(1)
annotation_colors[[colnames(annotation)[i]]] = hsv(r, c(0.1, 1), 1)
}
}
}
#set the baseline factor in each annotation to '#FFFFFF'
#if a factor is binary, set the next level to dark gray #222222
for(i in seq_along(annotation_colors)){
annotation_colors[[i]][1]<-"#FFFFFF"
if(length(annotation_colors[[i]])==2){
annotation_colors[[i]][2]<-"#222222"
}
}
return(annotation_colors)
}

kmeans_pheatmap = function(mat, k = min(nrow(mat), 150), sd_limit = NA, ...){
# Filter data
if(!is.na(sd_limit)){
Expand Down Expand Up @@ -547,6 +658,13 @@ kmeans_pheatmap = function(mat, k = min(nrow(mat), 150), sd_limit = NA, ...){
#' calculated so that the plot would fit there, unless specified otherwise.
#' @param width manual option for determining the output file width in inches.
#' @param height manual option for determining the output file height in inches.
#' @param row_annotation data frame that specifies the annotations shown on the
#' rows. Each row defines the features for a specific row. The rows in the data
#' and rows in the annotation are matched using corresponding row names. Currently only binary
#' categorical variables are supported with a default black and white color scheme. The category labels are
#' given by the data frame column names.
#' @param row_annotation_legend Not currently supported.
#' @param row_annotation_colors Not currently supported.
#' @param \dots graphical parameters for the text used in plot. Parameters passed to
#' \code{\link{grid.text}}, see \code{\link{gpar}}.
#'
Expand Down Expand Up @@ -585,10 +703,11 @@ kmeans_pheatmap = function(mat, k = min(nrow(mat), 150), sd_limit = NA, ...){
#'
#'
#' # Generate column annotations
#' annotation = data.frame(Var1 = factor(1:10 \%\% 2 == 0, labels = c("Class1", "Class2")), Var2 = 1:10)
#' annotation = data.frame(Var1 = factor(1:10 %% 2 == 0,
#' labels = c("Class1", "Class2")), Var2 = 1:10)
#' annotation$Var1 = factor(annotation$Var1, levels = c("Class1", "Class2", "Class3"))
#' rownames(annotation) = paste("Test", 1:10, sep = "")
#'
#'
#' pheatmap(test, annotation = annotation)
#' pheatmap(test, annotation = annotation, annotation_legend = FALSE)
#' pheatmap(test, annotation = annotation, annotation_legend = FALSE, drop_levels = FALSE)
Expand All @@ -600,15 +719,18 @@ kmeans_pheatmap = function(mat, k = min(nrow(mat), 150), sd_limit = NA, ...){
#'
#' ann_colors = list(Var1 = Var1, Var2 = Var2)
#'
#' pheatmap(test, annotation = annotation, annotation_colors = ann_colors, main = "Example with all the features")
#' #Specify row annotations
#' row_ann <- data.frame(Cytokines=gl(2,nrow(test)/2),`Transcription Factors`=relevel(gl(2,nrow(test)/2),"2"))
#' rownames(row_ann)<-rownames(test)
#' pheatmap(test, annotation = annotation, annotation_legend = FALSE, drop_levels = FALSE,row_annotation = row_ann)
#'
#' # Specifying clustering from distance matrix
#' drows = dist(test, method = "minkowski")
#' dcols = dist(t(test), method = "minkowski")
#' pheatmap(test, clustering_distance_rows = drows, clustering_distance_cols = dcols)
#'
#' @importFrom RColorBrewer brewer.pal
#' @export
pheatmap = function(mat, color = colorRampPalette(rev(c("#D73027", "#FC8D59", "#FEE090", "#FFFFBF", "#E0F3F8", "#91BFDB", "#4575B4")))(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", treeheight_row = ifelse(cluster_rows, 50, 0), treeheight_col = ifelse(cluster_cols, 50, 0), legend = TRUE, legend_breaks = NA, legend_labels = NA, annotation = NA, annotation_colors = NA, annotation_legend = TRUE, drop_levels = TRUE, show_rownames = T, show_colnames = T, main = NA, fontsize = 10, fontsize_row = fontsize, fontsize_col = fontsize, display_numbers = F, number_format = "%.2f", fontsize_number = 0.8 * fontsize, filename = NA, width = NA, height = NA, ...){
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", treeheight_row = ifelse(cluster_rows, 50, 0), treeheight_col = ifelse(cluster_cols, 50, 0), legend = TRUE, legend_breaks = NA, legend_labels = NA, annotation = NA, annotation_colors = NA, annotation_legend = TRUE, drop_levels = TRUE, show_rownames = T, show_colnames = T, main = NA, fontsize = 10, fontsize_row = fontsize, fontsize_col = fontsize, display_numbers = F, number_format = "%.2f", fontsize_number = 0.8 * fontsize, filename = NA, width = NA, height = NA, row_annotation = NA, row_annotation_legend = FALSE, row_annotation_colors=NA, ...){

# Preprocess matrix
mat = as.matrix(mat)
Expand Down Expand Up @@ -700,6 +822,12 @@ pheatmap = function(mat, color = colorRampPalette(rev(c("#D73027", "#FC8D59", "#
annotation = annotation[colnames(mat), , drop = F]
annotation_colors = generate_annotation_colours(annotation, annotation_colors, drop = drop_levels)
}

#Prepare row annotation colors
if(!is.na(row_annotation[[1]][1])){
row_annotation = row_annotation[rownames(mat), , drop=F]
row_annotation_colors = generate_row_annotation_colours(row_annotation,row_annotation_colors, drop = drop_levels)
}

if(!show_rownames){
rownames(mat) = NULL
Expand All @@ -710,7 +838,7 @@ pheatmap = function(mat, color = colorRampPalette(rev(c("#D73027", "#FC8D59", "#
}

# Draw heatmap
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 = annotation, annotation_colors = annotation_colors, annotation_legend = annotation_legend, main = main, fontsize = fontsize, fontsize_row = fontsize_row, fontsize_col = fontsize_col, fmat = fmat, fontsize_number = fontsize_number, ...)
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 = annotation, annotation_colors = annotation_colors, annotation_legend = annotation_legend, main = main, fontsize = fontsize, fontsize_row = fontsize_row, fontsize_col = fontsize_col, fmat = fmat, fontsize_number = fontsize_number, row_annotation = row_annotation, row_annotation_legend = row_annotation_legend, row_annotation_colors = row_annotation_colors, ...)

invisible(list(tree_row = tree_row, tree_col = tree_col, kmeans = km))
}
Expand Down
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