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kevinblighe / EnhancedVolcano

Publication-ready volcano plots with enhanced colouring and labeling
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Issue with 'selectLab' #60

Closed nbbarrientos closed 3 years ago

nbbarrientos commented 3 years ago

Hello,

First off, thank you for this tool. Very useful and very easy to use. I have a question regarding 'selectLab'. Instead of genes, I'm plotting introns but I still chose to label these introns with the gene name they are part of. However, because there are multiple introns within a gene, I also see the same label printed out multiple times. This is okay, except that when I use the selectLab option, it also prints the labels for introns that are not significant.

I was under the impression, based on the manual, that EnhancedVolcano will only print the labels for significant points (those that pass the -log10(p-value) and the log2(FC) thresholds) by default. Does selectLab override this when used? If so, is there a way to maintain the default printing of labels (to print only significant ones) when using selectLab?

Here's an example of what I'm getting: image

Thank you so much for your help. Nelson Barrientos

kevinblighe commented 3 years ago

Hi Nelson, Thank you for using this package.

Hmm, this problem is somewhat unique. Based on how the package is designed, when selectLab is activated, yes, it overrides the thresholds for -log10(p-value) and log2(FC).

In order to do what you want, unfortunately, you may have to manually change the names for the non-statistically significant introns for VCAM1 and TPM2. For example, change them [temporarily] to VCAM1ns and TPM2ns

Kind regards, Kevin

nbbarrientos commented 3 years ago

Hi Kevin,

Thank you for your quick response. I was thinking that might be the best course of action for now.

Best regards, Nelson