R: heatmap.2 doesn't generate symmetrical plot even I set symm=T

Question

I have matrix with the same rownames and colnames:Matrix

Then I use heatmap.2 to plot it symmetrically:

heatmap.2(matrix, Rowv=T, scale='none', dendrogram="row", symm =T, col = brewer.pal(9,"Reds"))

But I got the image as below:

It is not symmetrical at all. Can someone give me a suggestion?

Thanks,

sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.4 LTS

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

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

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

loaded via a namespace (and not attached):
 [1] htmltools_0.3.5    tools_3.3.1        yaml_2.1.13        Rcpp_0.12.5        KernSmooth_2.23-15
 [6] rmarkdown_0.9.6    gdata_2.17.0       knitr_1.13         caTools_1.17.1     digest_0.6.9      
[11] bitops_1.0-6       gtools_3.5.0

Pleas include your data using `dput()` rather then a dropbox link. — Roman, Jul 05 '16 at 15:07
Thx. This is my first time to ask question. How about this? [link](https://www.dropbox.com/s/c6ln0wojftno9hv/matrix?dl=0) — Joseph Kuo, Jul 05 '16 at 15:33

score 0 · Answer 1 · answered Jul 07 '16 at 09:30

0

This code solves my problem:

heatmap.2(m_up, Rowv=F, Colv="Rowv", scale='none', symm =T, col = brewer.pal(9,"Reds"))

answered Jul 07 '16 at 09:30

Joseph Kuo

1
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R: heatmap.2 doesn't generate symmetrical plot even I set symm=T

1 Answers1