How set Times New Roman text for Rows and Columns in a Heatmap In R

Question

I am making a Heatmap in R using Heatmap.2 and gplot. I want so that all the text, including the row and column names, along with the axis titles, are written in Times New Roman.

Here is the code I have so far:

install.packages("extrafont")
library(extrafont)
font_import()
loadfonts(device="pdf")      
fonts()
heatmap.2(data,Colv=NA, Rowv = NA, scale="row", tracecol = NA, col=terrain.colors(256),     xlab="Treatments", ylab="Genes of Interest", theme_bw(), theme(text=element_text(family="Times New Roman", face="bold", size=12)))

But unfortunately, this only makes the axis titles Times new Roman, nothing else. I was wondering if anybody knew how to make the rows and column titles the same?

Many thanks!

Answer 1

It is not clear to me whether you are trying to export a PDF file with the fonts, which should work with this example:

set.seed(1)
mat <- matrix(stats::runif(100, 3, 14), nrow = 10, ncol = 10,
              dimnames = list(paste0("Row", 1:10), paste0("Col", 1:10)))
pdf(file="font_plot.pdf", family="Times", width=6, height=6)
gplots::heatmap.2(mat, dendrogram = "none", scale="row", tracecol = NA, 
                  col=terrain.colors(256),
                  xlab="Treatments", ylab="Genes of Interest")

dev.off()
#> png 
#>   2

^{Created on 2020-06-29 by the reprex package (v0.3.0)}

... or whether you want the output to any graphics device (including the screen) to have those fonts.

Note that with heatmap.2 you are not dealing with ggplot2 (but grid ) graphics, therefore theming does not work the way you tried.

You have several options, including approaches using ggplot (involving geom_tile ), plotly , or the more configurable grid-based ComplexHeatmap package. An example for the latter is shown below:

set.seed(1)
mat <- matrix(stats::runif(100, 3, 14), nrow = 10, ncol = 10,
              dimnames = list(paste0("Row", 1:10), paste0("Col", 1:10)))

suppressPackageStartupMessages(library(ComplexHeatmap))
ht_opt(heatmap_column_names_gp = gpar(fontfamily = "Times"), 
       heatmap_row_names_gp = gpar(fontfamily = "Times"), 
       heatmap_column_title_gp = gpar(fontfamily = "Times"),
       heatmap_row_title_gp = gpar(fontfamily = "Times"),
       legend_title_gp = gpar(fontfamily = "Times"),
       legend_labels_gp = gpar(fontfamily = "Times"))

draw(Heatmap(t(scale(t(mat))), 
             cluster_columns=FALSE, cluster_rows = FALSE,
             heatmap_legend_param = list(title = "Row Z-score",
                                         direction = "horizontal", 
                                         title_position = "lefttop"),
             column_title="Treatments", column_title_side="bottom",
             row_title="Genes of Interest", row_title_side="right",
             col=terrain.colors(256)),
     heatmap_legend_side = "top")

^{Created on 2020-06-29 by the reprex package (v0.3.0)}