Question: ggheatmap R script error.
1
gravatar for user230613
4.2 years ago by
user230613280
Europe
user230613280 wrote:

Hi all,

I'm using this r script (https://cwcode.wordpress.com/2013/01/30/ggheatmap-version-2/ ) in order to perform a nice heatmap automatically. At the beginning, it works as expected, but if I increase the size of the dataset, it crashes. I'm not very good at R, I'm starting, so I don't know exactly what it is going on. I guess that maybe memory problems. This is the error message:

Error in grid.Call.graphics(L_upviewport, as.integer(n)) :
  cannot pop the top-level viewport ('grid' and 'graphics' output mixed?)
Error in grid.Call.graphics(L_upviewport, as.integer(n)) :
  cannot pop the top-level viewport ('grid' and 'graphics' output mixed?)
Error: evaluation nested too deeply: infinite recursion / options(expressions=)?
Error during wrapup: evaluation nested too deeply: infinite recursion / options(expressions=)?


Anyone can suggest me how to solve this issue? My input dataset has 62 columns and 16956 number of rows. If I extract the first 10000 rows, the script works OK.

Any help would be really appreciated.

R • 1.7k views
ADD COMMENTlink modified 4.2 years ago • written 4.2 years ago by user230613280

This is really a question more appropriate for R help resources because this is a problem with R, not a bioinformatics question.  

Can you please post your R code in your question so we can see what you are doing? I assume you're taking the code you grabbed from the link you provided and modifying it.

ADD REPLYlink modified 4.2 years ago • written 4.2 years ago by Josh Herr5.6k

Yes, maybe I should post this question on stackoverflow or some similar forum. I hope to find someone who had undergone this issue, or find here the script developer :). The code is on github (https://github.com/chr1swallace/random-functions/blob/master/R/ggplot-heatmap.R). I've not modified it.

ADD REPLYlink written 4.2 years ago by user230613280

http://stackoverflow.com/questions/29363172/ggheatmap-r-script-error

ADD REPLYlink written 4.2 years ago by zx87547.3k
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