Plotting CNV matrix as heatmap using python
1
0
Entering edit mode
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
ADD COMMENT
1
Entering edit mode

Take a look at matplotlib directly, or plot_ly has some nice heatmap functionality.

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode
ADD COMMENT

Login before adding your answer.

Traffic: 1880 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6