search

kevinblighe / EnhancedVolcano

Publication-ready volcano plots with enhanced colouring and labeling
399 stars 81 forks source link

dealing with zero pvalue #43

Closed MichaelPeibo closed 4 years ago

MichaelPeibo commented 4 years ago

Hi @kevinblighe I am using MAST to calculate scRNA-seq data. For top DEGs, there are extreme small pvalues(0.000000e+00), figure below. They will not be on the volcanoplot. Any suggestion how to plot them? image

kevinblighe commented 4 years ago

Hey Michael, the package should convert these to 10^-1 times the lowest non-zero p-value, and issue a warning message in doing so. Does that not happen in your case? Which version of the package are are you using?

You can see this elaborated in the following code chunk: https://github.com/kevinblighe/EnhancedVolcano/blob/master/R/EnhancedVolcano.R#L91-L111

Let me know!

MichaelPeibo commented 4 years ago

@kevinblighe Yes, you are right. I did not see it because I set a xlim and ylim. When I removed or enlarge them, I could see them now. Great package!

kevinblighe commented 4 years ago

Great! - thanks @MichaelPeibo