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Teichlab / cellphonedb

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Dot plot problem: Error in all_pval[match(selected_rows, intr_pairs), selected_columns] #372

Open Zaein opened 2 years ago

Zaein commented 2 years ago

Hey all,

I am running this code: cellphonedb plot dot_plot --means-path /home/schweir3/CellphoneDB/Results/means.txt --pvalues-path /home/schweir3/CellphoneDB/Results/pvalues.txt --output-path /home/schweir3/CellphoneDB/Results

And I am getting this error message:

R[write to console]: Error in all_pval[match(selected_rows, intr_pairs), selected_columns] : 
  incorrect number of dimensions
[ ][APP][05/05/22-15:34:09][ERROR] R Runtime Exception: Error in all_pval[match(selected_rows, intr_pairs), selected_columns] : 
  incorrect number of dimensions

Does anyone have any suggestions for solving this issue? I found nothing for Cellphone DB searching here and on Google. This does seem to be an issue with the conda environment and not CellPhone DB though.

Cheers,

Zaein commented 2 years ago

I was able to generate the Dot_Plot but when i click the pdf file I get a "Dot.Plot not found" error.

RSTAR553 commented 2 years ago

I meet this problem too!

RSTAR553 commented 2 years ago

my previous meta.txt Cell cell_type P2Res_B3_sc01 B cells P2Res_B3_sc02 B cells P2Res_B3_sc03 B cells P2Res_B3_sc04 B cells P2Res_B3_sc05 B cells P2Res_B3_sc06 B cells P2Res_B3_sc07 B cells P2Res_B3_sc08 B cells P2Res_B3_sc09 B cells

I think there should be at least 2 dimension(cell_type) to draw a dot plot, so I change my meta like this: rownames(sce@meta.data) seurat_clusters P2Res_B3_sc01 2 P2Res_B3_sc02 4 P2Res_B3_sc03 2 P2Res_B3_sc04 4 P2Res_B3_sc05 7 P2Res_B3_sc06 6 P2Res_B3_sc07 2 P2Res_B3_sc08 3 P2Res_B3_sc09 6

then my problem was solved. Hope this can help you~