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nuno-agostinho / cTRAP

Identification of candidate causal perturbations from differential gene expression data
https://nuno-agostinho.github.io/cTRAP
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cTRAP not working properly with demo data #47

Open A-Kaizeler-A opened 9 months ago

A-Kaizeler-A commented 9 months ago

Issue Summary

Hi Nuno,

I've encountered some issues with the cTRAP WebApp and the R package. Here are the details:

WebApp Issue:

The WebApp version of cTRAP, hosted here, is not working properly. After uploading Differentially Expression Data and loading cMAP Perturbations, attempting to perform an analysis by clicking on "Rank by similarity" results in the site getting a grey filter and loading indefinitely:

image

R Package Issue:

After following the R tutorial for the cTRAP R package, the plotTargetingDrugsVSsimilarPerturbations function is not working as intended:

plotTargetingDrugsVSsimilarPerturbations(predicted, compareCompounds, column="spearman_rank")

#Resulting on the following error
> Columns 'broad id' and 'pubchem_cid' were matched based on 0 common values; to manually select columns to compare, please set arguments starting with 'keyCol'

I encounter both these errors when using the default Differentially Expression Data (diffExprStat) from the R package.

Thank you for your attention and your help!

Best regards, Alex

nuno-agostinho commented 9 months ago

Hi @A-Kaizeler-A,

Thanks for reporting these issues!

I will check what is going on soon and come back to you.

Best, Nuno