Search code examples
rheatmapgplots

Removing white lines in colkey of a heatmap

I am trying to create a heatmap but the color key has some white lines.

Questions#1: How can I remove these white lines?The range should be from -100 to 100. Only "0" should be white in the color key.

Question#2: How can I remove the "X" in the column labels?

Here's my script:

library(gplots)
dat <- read.csv("Baguio.csv", header=TRUE)
mat_data<-data.matrix(dat)

my_palette <- colorRampPalette(c("blue","white","red"))(200)
breaks=c(seq(-100,-1,length=100),0,seq(1,100,length=100))

png("heatmap.png",    # create PNG for the heat map
 width = 5*300,        # 5 x 300 pixels
 height = 5*300,
 res = 300,            # 300 pixels per inch
 pointsize = 8)        # smaller font size

heatmap.2(mat_data,
 main = "test", # heat map title
 notecol="black",      # change font color of cell labels to black
 density.info="none",  # turns off density plot inside color legend
 trace="none",         # turns off trace lines inside the heat map
 margins =c(5,5),     # widens margins around plot
 col=my_palette,
 breaks=breaks,
 dendrogram="none",
 symkey=F, xlab="Year", ylab="Date",
 Colv="NA",Rowv="NA")            # turn off column clustering
dev.off()               # close the PNG device

Here's the link to the data: Data

Output Image

I'll appreciate any help.

Solution

  • Question 1: you could use read_csv from tidyverse package. It can use numbers as names.

    Question 2: I reproduced your code and my graphics is without white lines. Maybe you can increase the resolution?