Question

I have following matrix wanted to create heatmap in R

    E1  E2  P1   P2
E1  1   0.73867 0.865486 0.708944
E2      1   0.749623 0.949532
P1          1    0.747194
P2              1

I used following code to achieve it

acc<-read.csv("data.csv",header=TRUE,sep=",")

row.names(acc)<-acc[,1]

acc <- acc[,2:dim(acc)[2]]

acc_matrix<-data.matrix(acc)

acc_map <- heatmap_2(acc_matrix,Rowv=NA, Colv=NA, col = rev(heat.colors(256)),scale="none",legend=1)

But im getting error as follows

Error in `[.data.frame`(acc, , 1:dim(acc)[1]) : 
  undefined columns selected

Can anybody please help how to solve this…

Thanks

NI

Answer 1

Here’s one solution using the ggheat function.

mat <- matrix(NA,ncol=4,nrow=4)
diag(mat) <- 1
library(gdata)
upperTriangle(mat) <- runif(6)
colnames(mat) <- rownames(mat) <- c("E1","E2","P1","P2")
ggheat(mat)