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ventolab / CellphoneDB

CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.
https://www.cellphonedb.org/
MIT License
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cellphonedb heatmap with microenvironments #23

Closed Nasrine26 closed 2 years ago

Nasrine26 commented 2 years ago

Hello,

I am trying to use the plotting function heatmap after I've run cellphonedb statistical analysis with --microenvs and get the following error: 

Error in `[.data.frame`(all_intr, , pairs1[i]) :
  undefined columns selected

[ ][APP][11/03/22-14:05:41][ERROR] R Runtime Exception: Error in `[.data.frame`(all_intr, , pairs1[i]) :
  undefined columns selected

When I run the same code and perform statistical analysis without --microenvs, I get no error and am able to plot the heatmap. Is there an issue maybe in the heamap function when we use --microenvs?

Many thanks!

Nasrine26 commented 2 years ago

It's fine I've been able to plot by tweaking your code.

cchd0001 commented 2 years ago

It's fine I've been able to plot by tweaking your code.

I have encountered the same issue, could you please tell me how to modify the code ?