R pheatmap: change annotation colors and prevent graphics window from popping up

Question

Following up on this question, I found the pheatmap function (which offers me a lot more control on the stuff that I want to do than heatmap.2).

I have 2 problems though:

1- I cannot change the colors of the annotation (categories)

2- The graphics window keeps popping up even when I am saving the output in a png file

This is my MWE:

library(pheatmap)
library(RColorBrewer)
cols <- colorRampPalette(brewer.pal(9, "Set1"))

mymat <- matrix(rexp(600, rate=.1), ncol=12)
colnames(mymat) <- c(rep("treatment_1", 3), rep("treatment_2", 3), rep("treatment_3", 3), rep("treatment_4", 3))
rownames(mymat) <- paste("gene", 1:dim(mymat)[1], sep="_")

annotdf <- data.frame(row.names = paste("gene", 1:dim(mymat)[1], sep="_"), category = c(rep("CATEGORY_1", 10), rep("CATEGORY_2", 10), rep("CATEGORY_3", 10), rep("CATEGORY_4", 10), rep("CATEGORY_5", 10)))

mycolors <- cols(length(unique(annotdf$category)))
names(mycolors) <- unique(annotdf$category)
mycolors <- list(mycolors = mycolors)

pheatmap(mymat,
     color=greenred(75),
     scale="row",
     cluster_rows = FALSE,
     cluster_cols = FALSE,
     gaps_row=c(10,20,30,40),
     gaps_col=c(3,6,9),
     cellheight = 6,
     cellwidth = 20,
     border_color=NA,
     fontsize_row = 6,
     main="Genes grouped by categories",
     filename = "TEST.png",
     annotation_row = annotdf,
     annotation_colors = mycolors
)

Which produces:

As you can see, the colors are clearly NOT the Set1 palette I specify, but the default pheatmap colors (you will get the same results removing the annotation_colors line).

So my question here is: How do I specify annotation_colors in pheatmap??

On the other hand, even when I am saving the pheatmap output in a png file, the graphics window keeps popping up, how do I prevent this from happening?

Thanks!

> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.1 LTS

locale:
 [1] LC_CTYPE=en_SG.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_SG.UTF-8        LC_COLLATE=en_SG.UTF-8    
 [5] LC_MONETARY=en_SG.UTF-8    LC_MESSAGES=en_SG.UTF-8   
 [7] LC_PAPER=en_SG.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_SG.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] gplots_3.0.1       RColorBrewer_1.1-2 pheatmap_1.0.8    

loaded via a namespace (and not attached):
 [1] compiler_3.3.1     colorspace_1.2-6   scales_0.4.0       plyr_1.8.3        
 [5] tools_3.3.1        gtable_0.2.0       Rcpp_0.12.7        KernSmooth_2.23-15
 [9] gdata_2.17.0       grid_3.3.1         caTools_1.17.1     bitops_1.0-6      
[13] munsell_0.4.3      gtools_3.5.0

Ramer

mycolors2 <- list(category = brewer.pal(9, "Set1")[1:5]); names(mycolors2$category) <- levels(annotdf$category) (sorry, I don't have enough time to answer) – Epiphany

That is not extendable for cases with a number of categories >9. However, based on your comment, the following will take care of that situation: cols <- colorRampPalette(brewer.pal(5, "Set1")); mycols <- cols(length(unique(annotdf$category))); mycolors <- list(category=mycols); names(mycolors$category) <- levels(annotdf$category) – Ramer

There is still the matter of the graphics window popping out... – Ramer

And btw, how do you include code in the comments, like in your one above? – Ramer

to format code in the comments, or inline for that matter, with backticks " ` " – Geoff

Answer 1

1. To get more colors for more categories you will need to use a different color palette. There are many continuous palettes that will allow you to go well beyond 12 (like with RColorBrewer).

2. If you are running the code in your MWE as is, the R graphics window should not be popping up. I ran your example and it produced the desired file with out opening a graphics device to the console. Below is my sessioInfo() if you would like to compare. I would try closing all devices (graphics.off()) and then running your heatmap code to see if that solves the problem. I would also check to make sure you have write privileges in the directory you are currently working in???

3. As @cuttlefish stated in his comment to get the custom Row/Col colors to display the names in the list of colors has to mach the colnames of your annotation dataframe.

For more than 12 colors

mymat <- matrix(rexp(720, rate=.1), ncol=12)
colnames(mymat) <- c(rep("treatment_1", 3), rep("treatment_2", 3), rep("treatment_3", 3), rep("treatment_4", 3))
rownames(mymat) <- paste("gene", 1:dim(mymat)[1], sep="_")

annotdf <- data.frame(row.names = rownames(mymat), 
                      category = rep(paste0("Category_", seq(12)), each=5) )  

newCols <- colorRampPalette(grDevices::rainbow(length(unique(annotdf$category))))
mycolors <- newCols(length(unique(annotdf$category)))
names(mycolors) <- unique(annotdf$category)
mycolors <- list(category = mycolors)

pheatmap(mymat,
         color=greenred(75),
         scale="row",
         cluster_rows = FALSE,
         cluster_cols = FALSE,
         gaps_row=c(5,10,15,20,25,30,35,40,45,50, 55),
         gaps_col=c(3,6,9),
         cellheight = 6,
         cellwidth = 20,
         border_color=NA,
         fontsize_row = 6,
         main="Genes grouped by categories",
         filename = "TEST_12cat.png",
         annotation_row = annotdf,
         annotation_colors = mycolors
)

SessionInfo

R version 3.3.0 (2016-05-03)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.6 (El Capitan)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] pheatmap_1.0.8     RColorBrewer_1.1-2 gplots_3.0.1      

loaded via a namespace (and not attached):
 [1] colorspace_1.3-0   scales_0.4.1       colorRamps_2.3     plyr_1.8.4         tools_3.3.0       
 [6] gtable_0.2.0       Rcpp_0.12.7        KernSmooth_2.23-15 gdata_2.17.0       grid_3.3.0        
[11] caTools_1.17.1     munsell_0.4.3      bitops_1.0-6       gtools_3.5.0    

Geoff

The graphics window keeps popping up even on a fresh boot and fresh run with emacs... It's really annoying. I have included my sessionInfo() output in the question – Ramer

And a little question (I might start a new page for it): Do you know if it is possible to do clustering and show dendrograms PER CATEGORY? Thanks! – Ramer

Check it at #41648793 – Ramer

Does the image also get written to the file? I am not well versed in running r from emacs. And this information would have been nice to receive from the beginning as we all assume you are using the R console and not emacs. – Geoff

To show dendrograms per category you need to plot each category separately. If your categories are interleaved then that tells you something about the categories, imo. – Geoff

sorry, yes, I run it from emacs, and the image gets printed in the png perfectly, but still the graphics window pops up empty – Ramer