Plotting CNV matrix as heatmap using python
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3.1 years ago
roy.granit ▴ 880

I have a marix with chromosome location and copy number data which looks like this

 chr    start   cell_1  cell_2  cell_3
1   9997206 1.42    -0.25   -0.84
1   9997306 -0.47   -0.32   -0.34
1   9997406 -0.51   0.19    -2.06
1   9997506 0.23    -0.2    0.27
1   9997606 -0.41   -0.27   -2.02


I wish to plot this data as a heatmap using python.. I've tried to do this with 'seaborn' but that did not go very well.. I'd love to get some advice since I was not able to find good answers.

I guess I could do this in R or matlab, but since my upstream script is written in python I though to try my luck with python.

Thanks!

python heatmap cnv • 1.4k views
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Take a look at matplotlib directly, or plot_ly has some nice heatmap functionality.

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Ended using https://github.com/broadinstitute/infercnv which runs from R but has great functionality

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2.9 years ago
Renesh ★ 2.1k