rororo rororo - 9 months ago 55
R Question

R - heatmap.2 (gplots): change colors for breaks

I generated a heatmap using heatmap.2 of the gplots package:

library(gplots)
abc <-read.csv(file="abc.txt", header=T, sep="\t", dec=".")
abcm<-as.matrix(abc)
def <-read.csv(file="def.txt", header=T, sep="\t", dec=".")
defm<-as.matrix(def)
mean <-read.csv(file="mean.txt", header=T, sep="\t", dec=".")
meanm<-as.matrix(mean)
distance.row = dist(as.matrix(def), method = "euclidean")
cluster.row = hclust(distance.row, method = "average")
distance.col = dist(t(as.matrix(abc)), method = "euclidean")
cluster.col = hclust(distance.col, method = "average")
my_palette <- colorRampPalette(c("red", "yellow", "green"))(n = 299)
heatmap.2(meanm, trace="none", dendrogram="both", Rowv=as.dendrogram(cluster.row), Colv=as.dendrogram(cluster.col), margins = c(7,7), col=my_palette, main="mean(def+abc)", xlab="def clustering", ylab="abc clustering", na.color="white")
breaks = seq(0,max(meanm),length.out=100)
gradient1 = colorpanel( sum( breaks[-1]<=95 ), "black", "red" )
gradient2 = colorpanel( sum( breaks[-1]>95 ), "red", "green" )
hm.colors = c(gradient1,gradient2)
hm.colors = c(gradient1,gradient2)
heatmap.2(meanm, trace="none", dendrogram="both", Rowv=as.dendrogram(cluster.row), Colv=as.dendrogram(cluster.col), margins = c(7,7), breaks=breaks,col=hm.colors, na.color="white")


I slightly modified the part starting from
breaks
from here: How to assign your color scale on raw data in heatmap.2()

Now I want to make different colors for the following ranges:


  • 100-95

  • 95-65

  • 65-45

  • 45-0



The code from the link only provides a solution for 3 categories, but how do I implement that for 4?

my sample input here (this is semicolon-separated. The real example is tab-delimited)

sp1;sp2;sp3;sp4;sp5;sp6;sp7;Sp8;sp9;sp10
sp1;100.00;67.98;66.04;71.01;67.71;67.25;66.96;65.48;67.60;68.11
sp2;67.98;100.00;65.60;67.63;81.63;78.10;78.11;65.03;78.11;85.50
sp3;66.04;65.60;100.00;65.32;64.98;64.59;64.55;75.32;65.21;65.36
sp4;71.01;67.63;65.32;100.00;67.20;66.90;66.69;65.17;67.48;67.86
sp5;67.71;81.63;64.98;67.20;100.00;78.28;78.38;64.41;77.36;82.27
sp6;67.25;78.10;64.59;66.90;78.28;100.00;83.61;64.47;75.74;77.96
sp7;66.96;78.11;64.55;66.69;78.38;83.61;100.00;63.80;75.66;77.72
Sp8;65.48;65.03;75.32;65.17;64.41;64.47;63.80;100.00;65.63;64.59
sp9;67.60;78.11;65.21;67.48;77.36;75.74;75.66;65.63;100.00;77.78
sp10;68.11;85.50;65.36;67.86;82.27;77.96;77.72;64.59;77.78;100.00

Answer Source

You do not provide a reproducible example, so I had to guess for some parts.

### your data
mean <- read.table(header = TRUE, sep = ';', text = "
                 sp1;sp2;sp3;sp4;sp5;sp6;sp7;Sp8;sp9;sp10
                 sp1;100.00;67.98;66.04;71.01;67.71;67.25;66.96;65.48;67.60;68.11
                 sp2;67.98;100.00;65.60;67.63;81.63;78.10;78.11;65.03;78.11;85.50
                 sp3;66.04;65.60;100.00;65.32;64.98;64.59;64.55;75.32;65.21;65.36
                 sp4;71.01;67.63;65.32;100.00;67.20;66.90;66.69;65.17;67.48;67.86
                 sp5;67.71;81.63;64.98;67.20;100.00;78.28;78.38;64.41;77.36;82.27
                 sp6;67.25;78.10;64.59;66.90;78.28;100.00;83.61;64.47;75.74;77.96
                 sp7;66.96;78.11;64.55;66.69;78.38;83.61;100.00;63.80;75.66;77.72
                 Sp8;65.48;65.03;75.32;65.17;64.41;64.47;63.80;100.00;65.63;64.59
                 sp9;67.60;78.11;65.21;67.48;77.36;75.74;75.66;65.63;100.00;77.78
                 sp10;68.11;85.50;65.36;67.86;82.27;77.96;77.72;64.59;77.78;100.00")

### your code
library(gplots)
meanm <- as.matrix(mean)

### define 4 colors to use for the space between 5 breaks
col = c("green","blue","red","yellow")
breaks <- c(0, 45, 65, 95, 100)
heatmap.2(meanm, breaks = breaks, col = col)

This yields the following plot:

enter image description here

I hope it makes the essence of defining the breaks and the colors clear.

UPDATE with gradient

I filled your four wanted "zones" defined by the 5 breakpoints with color gradients. I invented something: yellow-green, green-blue, blue-darkblue, darkblue-black.

breaks = seq(0, max(meanm), length.out=100)

### define the colors within 4 zones
gradient1 = colorpanel( sum( breaks[-1]<=45 ), "yellow", "green" )
gradient2 = colorpanel( sum( breaks[-1]>45 & breaks[-1]<=65 ), "green", "blue" )
gradient3 = colorpanel( sum( breaks[-1]>65 & breaks[-1]<=95 ), "blue", "darkblue" )
gradient4 = colorpanel( sum( breaks[-1]>95 ), "darkblue", "black" )

hm.colors = c(gradient1, gradient2, gradient3, gradient4)

heatmap.2(meanm, breaks = breaks, col = hm.colors)

This yields the following graph:

enter image description here

Please let me know whether this is what you want.

Recommended from our users: Dynamic Network Monitoring from WhatsUp Gold from IPSwitch. Free Download