pheatmap 行名在左侧
2021-01-28 本文已影响0人
周运来就是我
需求如题，效果如下：
library(pheatmap)
library(grid)
library(gtable)
colors = c(seq(-5,-1,length=1000),seq(-.999999,.999999,length=1000),seq(1, 5,length=1000))
my_palette <- colorRampPalette(c("blue", "white", "red"))(n = 2999)
data.random <- data.frame(matrix(data=rnorm(150), ncol=15, nrow=10))
rownames(data.random) <- letters[1:10]
colnames(data.random) <- LETTERS[1:15]
# Modified pheatmap:::heatmap_motor
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, ...)
{
lo = pheatmap:::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, ...)
res = lo$gt
mindim = lo$mindim
if (!is.na(filename)) {
if (is.na(height)) {
height = convertHeight(gtable_height(res), "inches", valueOnly = T)
}
if (is.na(width)) {
width = convertWidth(gtable_width(res), "inches", valueOnly = T)
}
r = regexpr("\\.[a-zA-Z]*$", filename)
if (r == -1)
stop("Improper filename")
ending = substr(filename, r + 1, r + attr(r, "match.length"))
f = switch(ending, pdf = function(x, ...) pdf(x, ...),
png = function(x, ...) png(x, units = "in", res = 300,
...), jpeg = function(x, ...) jpeg(x, units = "in",
res = 300, ...), jpg = function(x, ...) jpeg(x,
units = "in", res = 300, ...), tiff = function(x,
...) tiff(x, units = "in", res = 300, compression = "lzw",
...), bmp = function(x, ...) bmp(x, units = "in",
res = 300, ...), stop("File type should be: pdf, png, bmp, jpg, tiff"))
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, ...)
grid.draw(gt)
dev.off()
return(gt)
}
if (mindim < 3)
border_color = NA
if (!is.na(main)) {
elem = pheatmap:::draw_main(main, fontsize = 1.3 * fontsize, ...)
res = gtable_add_grob(res, elem, t = 1, l = 3, name = "main",
clip = "off")
}
if (!pheatmap:::is.na2(tree_col) & treeheight_col != 0) {
elem = pheatmap:::draw_dendrogram(tree_col, gaps_col, horizontal = T)
res = gtable_add_grob(res, elem, t = 2, l = 3, name = "col_tree")
}
if (!pheatmap:::is.na2(tree_row) & treeheight_row != 0) {
elem = pheatmap:::draw_dendrogram(tree_row, gaps_row, horizontal = F)
res = gtable_add_grob(res, elem, t = 4, l = 1, name = "row_tree")
}
elem = pheatmap:::draw_matrix(matrix, border_color, gaps_row, gaps_col,
fmat, fontsize_number, number_color)
res = gtable_add_grob(res, elem, t = 4, l = 3, clip = "off",
name = "matrix")
if (length(labels_col) != 0) {
pars = list(labels_col, gaps = gaps_col, fontsize = fontsize_col,
hjust_col = hjust_col, vjust_col = vjust_col, angle_col = angle_col,
...)
elem = do.call(pheatmap:::draw_colnames, pars)
res = gtable_add_grob(res, elem, t = 5, l = 3, clip = "off",
name = "col_names")
}
if (length(labels_row) != 0) {
pars = list(labels_row, gaps = gaps_row, fontsize = fontsize_row,
...)
elem = do.call(pheatmap:::draw_rownames, pars)
res = gtable_add_grob(res, elem, t = 4, l = 3, clip = "off",
name = "row_names")
}
if (!pheatmap:::is.na2(annotation_col)) {
converted_annotation = convert_annotations(annotation_col,
annotation_colors)
elem = pheatmap:::draw_annotations(converted_annotation, border_color,
gaps_col, fontsize, horizontal = T)
res = gtable_add_grob(res, elem, t = 3, l = 3, clip = "off",
name = "col_annotation")
if (annotation_names_col) {
elem = pheatmap:::draw_annotation_names(annotation_col, fontsize,
horizontal = T)
res = gtable_add_grob(res, elem, t = 3, l = 4, clip = "off",
name = "col_annotation_names")
}
}
if (!pheatmap:::is.na2(annotation_row)) {
converted_annotation = convert_annotations(annotation_row,
annotation_colors)
elem = pheatmap:::draw_annotations(converted_annotation, border_color,
gaps_row, fontsize, horizontal = F)
res = gtable_add_grob(res, elem, t = 4, l = 2, clip = "off",
name = "row_annotation")
if (annotation_names_row) {
elem = pheatmap:::draw_annotation_names(annotation_row, fontsize,
horizontal = F, hjust_col = hjust_col, vjust_col = vjust_col,
angle_col = angle_col)
res = gtable_add_grob(res, elem, t = 5, l = 2, clip = "off",
name = "row_annotation_names")
}
}
annotation = c(annotation_col[length(annotation_col):1],
annotation_row[length(annotation_row):1])
annotation = annotation[unlist(lapply(annotation, function(x) !pheatmap:::is.na2(x)))]
if (length(annotation) > 0 & annotation_legend) {
elem = pheatmap:::draw_annotation_legend(annotation, annotation_colors,
border_color, fontsize = fontsize, ...)
t = ifelse(is.null(labels_row), 4, 3)
res = gtable_add_grob(res, elem, t = t, l = 6, b = 5,
clip = "off", name = "annotation_legend")
}
if (!pheatmap:::is.na2(legend)) {
elem = pheatmap:::draw_legend(color, breaks, legend, fontsize = fontsize,
...)
t = ifelse(is.null(labels_row), 4, 3)
res = gtable_add_grob(res, elem, t = t, l = 5, b = 5,
clip = "off", name = "legend")
}
return(res)
}
# Modified pheatmap:::lo
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, ...)
{
if (!is.null(coln[1]) | (!pheatmap:::is.na2(annotation_row) & annotation_names_row)) {
if (!is.null(coln[1])) {
t = coln
}
else {
t = ""
}
tw = strwidth(t, units = "in", cex = fontsize_col/fontsize)
if (annotation_names_row) {
t = c(t, colnames(annotation_row))
tw = c(tw, strwidth(colnames(annotation_row), units = "in"))
}
longest_coln = which.max(tw)
gp = list(fontsize = ifelse(longest_coln <= length(coln),
fontsize_col, fontsize), ...)
coln_height = unit(1, "grobheight", textGrob(t[longest_coln],
rot = angle_col, gp = do.call(gpar, gp))) + unit(10,
"bigpts")
}
else {
coln_height = unit(5, "bigpts")
}
if (!is.null(rown[1])) {
t = rown
tw = strwidth(t, units = "in", cex = fontsize_row/fontsize)
if (annotation_names_col) {
t = c(t, colnames(annotation_col))
tw = c(tw, strwidth(colnames(annotation_col), units = "in"))
}
longest_rown = which.max(tw)
gp = list(fontsize = ifelse(longest_rown <= length(rown),
fontsize_row, fontsize), ...)
rown_width = unit(1, "grobwidth", textGrob(t[longest_rown],
rot = 0, gp = do.call(gpar, gp))) + unit(10, "bigpts")
}
else {
rown_width = unit(5, "bigpts")
}
gp = list(fontsize = fontsize, ...)
if (!pheatmap:::is.na2(legend)) {
longest_break = which.max(nchar(names(legend)))
longest_break = unit(1.1, "grobwidth",
textGrob(as.character(names(legend))[longest_break],
gp = do.call(gpar, gp)))
title_length = unit(1.1, "grobwidth", textGrob("Scale",
gp = gpar(fontface = "bold", ...)))
legend_width = unit(12, "bigpts") + longest_break * 1.2
legend_width = max(title_length, legend_width)
}
else {
legend_width = unit(0, "bigpts")
}
if (is.na(main)) {
main_height = unit(0, "npc")
}
else {
main_height = unit(1.5, "grobheight", textGrob(main,
gp = gpar(fontsize = 1.3 * fontsize, ...)))
}
textheight = unit(fontsize, "bigpts")
if (!pheatmap:::is.na2(annotation_col)) {
annot_col_height = ncol(annotation_col) * (textheight +
unit(2, "bigpts")) + unit(2, "bigpts")
t = c(as.vector(as.matrix(annotation_col)), colnames(annotation_col))
annot_col_legend_width = unit(1.2, "grobwidth", textGrob(t[which.max(nchar(t))],
gp = gpar(...))) + unit(12, "bigpts")
if (!annotation_legend) {
annot_col_legend_width = unit(0, "npc")
}
}
else {
annot_col_height = unit(0, "bigpts")
annot_col_legend_width = unit(0, "bigpts")
}
if (!pheatmap:::is.na2(annotation_row)) {
annot_row_width = ncol(annotation_row) * (textheight +
unit(2, "bigpts")) + unit(2, "bigpts")
t = c(as.vector(as.matrix(annotation_row)), colnames(annotation_row))
annot_row_legend_width = unit(1.2, "grobwidth", textGrob(t[which.max(nchar(t))],
gp = gpar(...))) + unit(12, "bigpts")
if (!annotation_legend) {
annot_row_legend_width = unit(0, "npc")
}
}
else {
annot_row_width = unit(0, "bigpts")
annot_row_legend_width = unit(0, "bigpts")
}
annot_legend_width = max(annot_row_legend_width, annot_col_legend_width)
treeheight_col = unit(treeheight_col, "bigpts") + unit(5,
"bigpts")
treeheight_row = unit(treeheight_row, "bigpts") + unit(5,
"bigpts")
if (is.na(cellwidth)) {
mat_width = unit(1, "npc") - rown_width - legend_width -
treeheight_row - annot_row_width - annot_legend_width
}
else {
mat_width = unit(cellwidth * ncol, "bigpts") + length(gaps_col) *
unit(4, "bigpts")
}
if (is.na(cellheight)) {
mat_height = unit(1, "npc") - main_height - coln_height -
treeheight_col - annot_col_height
}
else {
mat_height = unit(cellheight * nrow, "bigpts") + length(gaps_row) *
unit(4, "bigpts")
}
gt = gtable(widths = unit.c(treeheight_row, rown_width,
mat_width, treeheight_row, legend_width, annot_legend_width),
heights = unit.c(main_height, treeheight_col, annot_col_height,
mat_height, coln_height), vp = viewport(gp = do.call(gpar,
gp)))
cw = convertWidth(mat_width - (length(gaps_col) * unit(4,
"bigpts")), "bigpts", valueOnly = T)/ncol
ch = convertHeight(mat_height - (length(gaps_row) * unit(4,
"bigpts")), "bigpts", valueOnly = T)/nrow
mindim = min(cw, ch)
res = list(gt = gt, mindim = mindim)
return(res)
}
# Modified pheatmap:::draw_rownames
draw_rownames <- function (rown, gaps, ...)
{
coord = pheatmap:::find_coordinates(length(rown), gaps)
y = unit(1, "npc") - (coord$coord - 0.5 * coord$size)
res = textGrob(rown, x = unit(-3, "bigpts"), y = y, vjust = 0.5,
hjust = 1, gp = gpar(...))
return(res)
}
assignInNamespace(x="draw_rownames", value=draw_rownames, ns="pheatmap")
assignInNamespace(x="lo", value=lo, ns="pheatmap")
assignInNamespace(x="heatmap_motor", value=heatmap_motor, ns="pheatmap")
?pheatmap
test = matrix(rnorm(200), 20, 10)
test[1:10, seq(1, 10, 2)] = test[1:10, seq(1, 10, 2)] + 3
test[11:20, seq(2, 10, 2)] = test[11:20, seq(2, 10, 2)] + 2
test[15:20, seq(2, 10, 2)] = test[15:20, seq(2, 10, 2)] + 4
colnames(test) = paste("Test", 1:10, sep = "")
rownames(test) = paste("Gene", 1:20, sep = "")
h <- pheatmap(test,
cluster_rows=T,
cluster_cols=T,
legend=TRUE,
color=my_palette,
breaks=colors,
show_rownames=TRUE,
show_colnames=TRUE
)
