How to save a heat map created using the ComplexHeatmap package to png format?

user_14886040 0
Viewed 4175

I have made a heatmap using the ComplexHeatmap package in R. I wanted to save the map on my pc and I run the following code:

df <- read.csv("/home/aahm/filename.csv")
View(df)

df1<- t(df[,2:ncol(df)])
colnames(df1) <- df[,1]
View (df1)
df2 <- scale(df1)

library(ComplexHeatmap)
library(RColorBrewer)
library(circlize)
mycols <- colorRamp2(breaks = c(0, 0.2, 0.4, 0.6, 1.0), 
                     colors = c('white', "green", "red", "magenta", "blue"))

png(file="/home/aahm/Desktop/filename_heatmap.png")
Heatmap(df1, width = unit(15, "cm"),
        name = "nucleotide diversity scores",
        row_names_gp = gpar(fontsize = 7), column_title = "Nucleotide Positions", row_title = '1000 Genomes populations',
        column_title_side = "bottom",
        col = mycols,
        show_column_dend = FALSE, cluster_rows = FALSE,
        column_order = order(as.numeric(gsub("column", "", colnames(df1)))),
        column_names_rot = 45,
)
dev.off()

An empty textfile with extension .png is created on my desktop rather than a png file with the map. Can someone help me find out what is wrong with my code?

r save
2 Answers

According to ComplexHeatmap guide (https://jokergoo.github.io/ComplexHeatmap-reference/book/a-single-heatmap.html) you just need to save you heatmap as a new variable and then use draw() function to create plot in the pdf file.

 png(file="/home/aahm/Desktop/filename_heatmap.png")
 ht <- Heatmap(...)
 draw(ht)
 dev.off()

You may also use some additional arguments of Heatmap function such as use_raster, raster_quality, raster_resize_mat, raster_by_magick, etc.

user_181213050

The sequence of the code should be like this

png("test.png",width=3.25,height=3.25,units="in",res=1200)

Your heat-map code

dev.off()

UPDATE

Save with your required dimension. You need to try which resolution is best for you.

png("test.png",width=3.25,height=3.25,units="in",res=1200)
user_140106530
Related