heatmap with values (ggplot2)

49
votes

I've seen heatmaps with values made in various R graphics systems including lattice and base like this:

enter image description here

I tend to use ggplot2 a bit and would like to be able to make a heatmap with the corresponding cell values plotted. Here's the heat map and an attempt using geom_text:

library(reshape2, ggplot2)
dat <- matrix(rnorm(100, 3, 1), ncol=10)
names(dat) <- paste("X", 1:10)
dat2 <- melt(dat, id.var = "X1")
p1 <- ggplot(dat2, aes(as.factor(Var1), Var2, group=Var2)) +
    geom_tile(aes(fill = value)) +
    scale_fill_gradient(low = "white", high = "red") 
p1

#attempt
labs <- c(apply(round(dat[, -2], 1), 2, as.character))
p1 +  geom_text(aes(label=labs), size=1)

Normally I can figure out the x and y values to pass but I don't know in this case since this info isn't stored in the data set. How can I place the text on the heatmap?

2
rggplot2
this question has an example of using text with geom_tile that may be useful. Move your aes() call from geom_tile to geom_text – SlowLearner
try heatmap.2. refer to similar post stackoverflow.com/questions/3789549/… – Puriney
@SlowLearner, worked perfectly. Thank you. – Tyler Rinker
@TylerRinker Had just hopped on the bus, couldn't provide a proper answer but glad to see you were able to get it sorted. – SlowLearner
Does this help? socialdatablog.com/heatmap-tables-with-ggplot2-sort-of – Roman Luštrik

2 Answers

100
votes

This has been updated to conform to tidyverse principles and improve poor use of ggplot2

Per SlowLeraner's comment I was easily able to do this:

library(tidyverse)

## make data
dat <- matrix(rnorm(100, 3, 1), ncol=10)

## reshape data (tidy/tall form)
dat2 <- dat %>%
    tbl_df() %>%
    rownames_to_column('Var1') %>%
    gather(Var2, value, -Var1) %>%
    mutate(
        Var1 = factor(Var1, levels=1:10),
        Var2 = factor(gsub("V", "", Var2), levels=1:10)
    )

## plot data
ggplot(dat2, aes(Var1, Var2)) +
    geom_tile(aes(fill = value)) + 
    geom_text(aes(label = round(value, 1))) +
    scale_fill_gradient(low = "white", high = "red")

enter image description here

6
votes

There is another simpler way to make heatmaps with values. You can use pheatmap to do this. 

dat <- matrix(rnorm(100, 3, 1), ncol=10)
names(dat) <- paste("X", 1:10)
install.packages('pheatmap') # if not installed already
library(pheatmap)
pheatmap(dat, display_numbers = T)

This will give you a plot like this

Heatmap with values

If you want to remove clustering and use your color scheme you can do

pheatmap(dat, display_numbers = T, color = colorRampPalette(c('white','red'))(100), cluster_rows = F, cluster_cols = F, fontsize_number = 15)

heatmap without clustering and red white colors

You can also change the fontsize, format, and color of the displayed numbers.