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I've seen heatmaps with values made in various R graphics systems including lattice and base like this:
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?
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To create a heatmap with the melted data so produced, we use geom_tile() function of the ggplot2 library. It is essentially used to create heatmaps.
Heat map with geom_tile A heap map in ggplot2 can be created with geom_tile , passing the categorical variables to x and y arguments and the continuous variable to fill argument of aes . Note that depending on the plotting windows size the tiles might not be squared. If you want to keep them squared use cood_fixed .
Let's use the heatmaply package in R to plot a correlation heatmap using the heatmaply_cor( ) function. Correlation of the data is the input matrix with “Features” column as x and y axis parameters. Function: heatmaply_cor(x, limits = c(-1, 1), xlab, ylab, colors = cool_warm,k_row, k_col …)
A basic heatmap can be produced using either the R base function heatmap() or the function heatmap. 2() [in the gplots package]. The pheatmap() function, in the package of the same name, creates pretty heatmaps, where ones has better control over some graphical parameters such as cell size.
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") 
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