Superimpose 2 Heatmaps

Question

[datanerd]

I need to superimpose two heatmaps. Any tools other than Matlab? Thanks in advance!

[Irsan]

Why don't you create a third matrix m3 where the z-values are calculated by summing/substracting the z-values from the m1 and m2?

[Josh Herr]

Can you elaborate on what you are interested in doing? A heatmap in multiple dimensions or a correlation of two heat maps?

[datanerd]

Hi, I have same dimension 2 heatmaps from 2 different studies, with the same exact row and columns. I want to overlay them , so to visualize the resultant effect (colors multiply) please let me know if am still not clear.

Answer 1

[Pavel Senin]

what about this approach?

library(reshape)
library(ggplot2)
library(scales)
library(gridExtra)

data1 <- matrix(runif(9),ncol=3,dimnames=list(c("A","B","C"),c("D","E","F")))
data1.m = melt(data1)
p1 <- ggplot(data1.m, aes(X1, X2)) + geom_tile(aes(fill=value), colour="white") +
  scale_fill_gradient(low = "white", high = "steelblue") + ggtitle("data 1")

data2 <- matrix(runif(9),ncol=3,dimnames=list(c("J","K","L"),c("P","Q","R")))
data2.m = melt(data2)
p2 <- ggplot(data2.m, aes(X1, X2)) + geom_tile(aes(fill=value), colour="white") +
 scale_fill_gradient(low = "white", high = "steelblue") + ggtitle("data 2")

d=rescale(data1+data2)
rownames(d)=paste(rownames(data1),rownames(data2))
colnames(d)=paste(colnames(data1),colnames(data2))
d.m = melt(d)
p3 <- ggplot(d.m, aes(X1, X2)) + geom_tile(aes(fill=value), colour="white") +
  scale_fill_gradient(low = "white", high = "steelblue") + ggtitle("data 1 + data 2")

print(arrangeGrob(p1, p2, p3, ncol=1))

[datanerd]

looks exactly what i was looking for. Thank you so much Seninp! Will try this.

[Pavel Senin]

you are very welcome :).

[zizigolu]

hello,

suppose that i have already downloaded GSE63706 and normalized that and i have a normalized text file now. and i have also a list of probsets (a text file of my interest probsets) in this array...i want to have a heat map showing the expression pattern of my interest probsets in this array, for example in this array i have 4 varieties and different tissues (rind and flesh) and phases (0,10,20,30,40 and 50 days after harvesting). heat maps showing the expression pattern of my probsets in varieties, tissues and phases i mean

please..