Hi I may have missed this but I saw every way to differentially color points based on FC or pval etc, but how do you differentially color just the labeled points? Thanks!
Hey,
If you mean to colour differently the points that are labeled automatically internally via ggrepel, then that is not possible in the current setup, and would likely involve a major overhaul of the internal coding.
If, however, you mean to colour points based on labels that you are supplying via the selectLab parameter, the you can neither do that directly; however, you can set-up a key-value pairing like I do here: Over-ride colouring scheme with custom key-value pairs
So, you would have to create a key-value pairing that distinguishes the points that you are asking it to label specifically.
Kevin
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version 2.3.6
Yes Im asking about the latter, points labeled via
selectLab.So is the key-value pairing possible if the points are spread around in different FC and pval quadrants? Thanks.
Indeed, it is independent of FC and p-value. If the point that you are labeling is in a very crowded space, though, then it may not become visible, depending on when it is placed in the plot space. This package just utilises the ggplot2 engine; so, it goes from the first to last row from your input data-frame when plotting. If your point is being crowded out, you can simply put it last in your input data-frame in order to ensure that it is always plot last (and on top of other points in the vicinity).
Great thanks for info! One final questions as regards p-value, is there a way to use the FDR output of DESeq2 instead of p-value as a cutoff in the plot?
Oh yeh, I mean, you can select any column for plotting on the y-axis; so, you can simply choose the FDR-adjusted p-values. In this case, the cut-off line will simply be drawn at
-log10(cutoff).There is no distinction made between adjusted and un-adjusted, really.