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wencke / wencke.github.io

GOplot
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chord_dat function throwing error #11

Open charlesfoster opened 5 years ago

charlesfoster commented 5 years ago

I've followed the outline of GOplot to create the circ object from my own data. The GOBar and GOBubble plots work. However, I can't do the chord plot. I get this error when using the chord_dat function:

chord <- chord_dat(circ, genes,terms)

Error in [<-(*tmp*, g, p, value = ifelse(M[g] %in% sub2$genes, 1, : subscript out of bounds"

Any suggestions for what is going wrong?

Thanks

vince-fang commented 1 year ago

I think you may check your gene names. I got the same error as you are. And I found those gene names had been changed to upper case.

Nhien198 commented 1 year ago

Thank you very much for your email!I am not online now, I will reply you as soon as possible.Best wish, 

Meghathippanna commented 10 months ago

I had come up with the same error. Imagining you have results from gprofiler, solution 1: results from the gprofiler may have Ensembl id's or gene names. Use the same format in the genes section of [chord <- chord_dat(circ, genes,terms)]

solution2: your choice of genes or ensembl id's should be from the "intersections" section of gprofiler results and similarly your choice of terms should be from the "term_name" section of gprofiler results

I've followed the outline of GOplot to create the circ object from my own data. The GOBar and GOBubble plots work. However, I can't do the chord plot. I get this error when using the chord_dat function:

chord <- chord_dat(circ, genes,terms)

Error in [<-(*tmp*, g, p, value = ifelse(M[g] %in% sub2$genes, 1, : subscript out of bounds"

Any suggestions for what is going wrong?

Thanks

Nhien198 commented 10 months ago

Thank you very much for your email!I am not online now, I will reply you as soon as possible.Best wish,