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Teichlab / cellphonedb

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undefined columns selected when running heatmap plotting #219

Open Sa753 opened 3 years ago

Sa753 commented 3 years ago

Hi ,

I got an error when I run plot heat map

undefined columns selected

I used the same meta.txt file that I used to run cellphonedb initially so I am not sure why it can't find the columns

Could you please help?. I saw that issue was raised before but it was closed with no reply so maybe they find an answer

Thanks

dianadom commented 3 years ago

I have the same issue. I run the heat map and I have got undefined columns selected.

CollapsarSpectrum commented 3 years ago

I replaced the symbols(/-_ et al) with dot(.) in cell/cluster names, and then the heatmap plot function works again. May it can help you.

msalaciak commented 3 years ago

I have this issue as well, I've replaced all symbols as mentioned above and still have this issue. Any tips to debug?

Thanks!

DrMaestre commented 3 years ago

I have the issue too.

prete commented 3 years ago

@msalaciak @DrMaestre could you provide sample files to reproduce this error? (meta.txt, means.txt and pvalues.txt)

user12Abio commented 3 years ago

According to CellPhoneDB website (https://www.cellphonedb.org/explore-sc-rna-seq), if your meta file is in .csv format it should be comma separated; if your meta file is in .txt, .tsv, .tab format then it should be tab separated

GuillermoWizard commented 3 years ago

I was getting this error too in Rcircos, It turned out that my chromosome names in my histogram data didn't match the ones on the ideogram.