I'm trying to generate a simple heatmap that has each row and column
separated by a black line. However, for some reason this only happens
for the first and last color. The middle color in my colorpanel()
command has an addition horizontal and vertical line that I would like
to get rid off when plotted using heatmap.2(). Any suggestions as to why I see these lines?
library(gplots)
my.matrix <- cbind(func.1 = c(1,2,2,1,1,3,1,2,3,1,1,2,2,3,1), func.2 =
c(2,2,1,1,3,3,1,1,2,2,1,3,3,2,1))
mycol <- colorpanel(n=3,"green","grey","red")
heatmap.2(my.matrix,Rowv=FALSE, Colv="Rowv", col=mycol, trace="both",
tracecol="black", key=FALSE, symm=FALSE, vline=NULL, hline=NULL)
link to the plot I get: https://dl.dropbox.com/u/8900971/heatmap.png
There's probably a way to do what you want but when I read your last comment my mind went to ggplot2. You didn't say it has to be a heatmap.2 solution so here's a ggplot2 one. Though I'm assuming the gplots version is of mor interest:
library(reshape2, ggplot2)
dat <- melt(my.matrix)
ggplot(dat, aes(x=Var2,y=Var1))+
geom_tile(aes(fill = value),colour='black') +
scale_fill_gradientn(colours=c("green","gray","red"),
values = rescale(c(min(dat$value), 1000, max(dat$value)))) +
coord_equal()