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Old 08-20-2013, 07:43 AM   #1
crazyhottommy
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Location: Gainesville

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Default what's wrong with heatmap.2, heatmap turns to blue after finishing plotting

Hi everyone,

I was plotting a transcription factor ChIP-seq data at TSS with heatmap.2

http://s24.postimg.org/njywavo7p/Selection_015.png

the problem is that the plot becomes blue after plotting as the green-red colour setting.
if you resize the window, you can see the red signal enriched at the TSS, but once finished plotting, the blue spread to the whole figure and I could not see anything...

See the picture above.

what's wrong with heatmap.2?
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Old 08-20-2013, 08:46 AM   #2
rboettcher
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I don't think this is a problem of the heatmap function, but more of your system. It seems that your data matrix is quite huge, so may I ask on what kind of hardware you are creating this heatmap? It may be that your RAM is too small or your graphics card simply cannot handle this much output.
As a possible solution: have you tried to save the plot to file directly and to open the file afterwards?
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Old 08-20-2013, 09:57 AM   #3
crazyhottommy
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Quote:
Originally Posted by rboettcher View Post
I don't think this is a problem of the heatmap function, but more of your system. It seems that your data matrix is quite huge, so may I ask on what kind of hardware you are creating this heatmap? It may be that your RAM is too small or your graphics card simply cannot handle this much output.
As a possible solution: have you tried to save the plot to file directly and to open the file afterwards?
yes, I tried to save it first, and after open it, it is still covered by blue.

The matrix is somewhat large, with 1728 rows and 601 columns, but many of them are 0s.

computer info:
Ubuntu 12.04 (precise)
Intel(R) Core(TM) i5-2520M CPU @ 2.50GHz
4G memory

I will try to run it on High performance cluster in our school to see if it has the same problem. Thanks!
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Old 08-20-2013, 11:02 AM   #4
crazyhottommy
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solved in Biostar.

I need to put the trace="none" when I plot the heatmap
Thanks.
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