Enhanced Volcano alter colAlpha for subset

Question

[noa.golan]

Hello,

I'm trying to plot my RNAseq data using Enhanced volcano. I'm trying to get genes in a pathway to be a different color. I'm able to alter their color, but it's hard to see them since they are covered by other points.

Is there a way to change ColAlpha for my pathway genes to 1 and all other genes to 0.2? And to bring them to the foreground?

Thanks!

Answer 1

[Kevin Blighe]

Hey, it is not possible to have colAlpha different for different groups. As you can imagine, there comes a point when certain regions of the plot space become so overcrowded.

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You can have different shapes for different groups, for example, use a small shape for one group and a large shape for another - I believe you can even specify "." for one group. Here are all shapes:

[source: http://sape.inf.usi.ch/quick-reference/ggplot2/shape]

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You can also highlight certain genes, almost like drawing on the plot space with a marker - take a look at the vignette, here: 4.12 Shade certain transcripts

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However, here is the best solution: if you want to give 'priority' to certain genes in the plot space, then you just need to ensure that they are plot last. So, before you do anything, re-order your input data-frame such that your gene(s) of interest are positioned in the last row(s). This will ensure that they are plot last, thus, over any other points.

Kevin

[noa.golan]

Thanks! This was incredibly helpful.

[Kevin Blighe]

Sure thing! Well, I developed the package, so, I ought to know