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I would like to know if it is possible to make a heatmap with 200k rows? I have a matrix with genomic coordinates as rows and each column represents the presence or absence of that region in each patients. so I have 15 patient (columns). Now when I am trying heatmap.2 or pheatmap I get the memory allocation problem, how will I be able to use the entire matrix to generate a heatmap. The values of my matrix are jsut 0 and 1 and I want to draw some hypothesis based on the heatmap. How will I be able to use it. I tried once on my laptop but it does not help , so I tried in our linux cluster which is quite powerful. But still shows the below error. How can I resolve this problem. I also add the sessionInfo() . Any workaround is appreciated

data<-read.delim("path/H3_marks_map.txt",sep="\t", row.names=1)
pdf(file="path/map/H3_maps1.pdf")
pheatmap(data,scale="none")
Error: cannot allocate vector of size 170.5 Gb
dev.off()

sessionInfo()                           
R version 3.1.2 (2014-10-31)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=C             LC_NUMERIC=C           LC_TIME=C.UTF-8       
 [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8   
 [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C          
[10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C   

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

other attached packages:
[1] RColorBrewer_1.1-2 pheatmap_1.0.7    

loaded via a namespace (and not attached):
[1] colorspace_1.2-6 grid_3.1.2       gtable_0.1.2     munsell_0.4.2   
[5] plyr_1.8.3       Rcpp_0.12.1      scales_0.3.0     tools_3.1.2
ivivek_ngs
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  • try `image` (either base graphics or raster). each point value can be turned to a color. – hrbrmstr Oct 15 '15 at 16:40
  • Infact my matrix has binary values, just 0 and 1 to show presence or absence of some biological marks.. still I would like to try the r package image. thanks a lot. Also my rows are not gene names they are genomic coordinates – ivivek_ngs Oct 16 '15 at 10:07

0 Answers0