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interactivereport / cellxgene_VIP

Enables cellxgene to generate violin, stacked violin, stacked bar, heatmap, volcano, embedding, dot, track, density, 2D density, sankey and dual-gene plot in high-resolution SVG/PNG format. It also performs differential gene expression analysis and provides a Command Line Interface (CLI) for advanced users to perform analysis using python and R.
https://cellxgenevip-ms.bxgenomics.com
MIT License
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Error while plotting ComplexHeatmap #76

Open ankur-26197 opened 2 years ago

ankur-26197 commented 2 years ago

Hello, I am using cellxgene VIP for plotting heatmap for gene expressions for different annotations loaded. I get the following error while selecting Complex heatmap

ERROR @server: Traceback (most recent call last): subprocess.CalledProcessError: Command '/opt/conda/envs/VIP/lib/python3.8/site-packages/server/app/complexHeatmap.R /tmp/HEAT1653565712.456287.csv IL3RA,FCGR2B,FCGR3B Expression False 6 8 Reds png 11 150 fontsize=4,col=\'black\',fontface=\'plain\' fontsize=4 fontsize=6 T Yes returned non-zero exit status 1.

However with seaborn it works perfectly fine and I could generate the heatmap.

Also when I set Gene as radio button to Row, it still plots them across column. Refer the image below for this issue.

seaborn_heatmap

I have deployed the application using docker.

Can you please help me out?

ankur-26197 commented 2 years ago

I found the solution for ComplexHeatmap. There were few dependencies missing.

yalayoubi commented 1 year ago

I found the solution for ComplexHeatmap. There were few dependencies missing.

what dependencies were missing? I am getting the same error