search

Teichlab / cellphonedb

MIT License
341 stars 105 forks source link

cellphonedb hestmap error #169

Closed khandaud15 closed 4 years ago

khandaud15 commented 4 years ago

Hi, thanks for developing such a nice tools. I am currently using it for scrnaseq datatset. I ran statistical analysis with the metadata file and count file. I got the outputs for that , but when I am trying to make the heatmap plot for the results. I am getting an weird error. I am using the same metadata file which i used to running statistical analyisis. can you please help me with an issue

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

I am using this cammand cellphonedb plot heatmap_plot scrna-meta.txt --pvalues-path pvalues.txt --output-path CellPhoenDb-output --count-name heatmap_count.pdf

my metadata has 2 columns like you mentioned

Thanks in advance

weiiioyo commented 4 years ago

Hi, I met the same issue. Have you solved it?

Sa753 commented 3 years ago

Hi I am getting the same error

Error in [.data.frame(all_intr, , pairs1[I]) undefined column selected

Any suggestions please?

berixD commented 3 years ago

I could solved the error by updating my meta.data file. Due to subsampling, some celltypes were not present in my pvalue file. So, I removed these celltypes from my meta.data file in order to plot the heatmap. The error ocurred in line33: n1 = intr_pairs[which(all_intr[,pairs1[i]]<=pvalue)]

object pairs is derived form the metadata file and all_intr is derived from the pvalue file. The subsampling issue may also explain why the error is not easily reproducible.