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Report volcano plot will now also plot points with pval 0 #229
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E.g. see this report: SRP254919_zero.html.zip |
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I'm not sure if the example report was to only show how the new p-value=0 threshold on the volcano plot would look like or to show a complete working example. If the former, then it looks great. If the latter, there are a few issues:
After reviewing the code, I couldn't find the reason for these issues, but I'm also not familiar with this codebase. |
@kdivilov It was mainly there for showing what the plot looks like, but the example is also working actually. RP23-4H14.1 is not DE according to the tables, why would you expect it to be marked as DE? I just had a look at the DE table, its entry is
Also, sorry for the confusion, the tables below the plots are rounded. The entries where it says padj 0 aren't actually 0, but a very small number. I've attached the report again, this time just without rounding: |
I'm not 100% sold on this. The data are fundamentally outside the axes, and inventing a p value ceiling such that we can show such points as a smear at the extremes of the plot doesn't add much to my mind. The tables are there to see the gene lists. @WackerO we might want to refine the rounding logic you added to the reporting to use scientific notation rather than marking non-0 p values as 0. |
I can definitely change the rounding so that the table is clearer, but I would like to argue in favor of the ceiling. This is something that is for example also done by gprofiler (clicking on Do you have a specific reason why you don't want these points added to the plot? @pinin4fjords |
Because such points can't be represented properly, they are by definition outside the plot boundaries. You can't just define an arbitrary ceiling- another point could come along with a lower p value than the ceiling. So you'd probably have to set a ceiling equal to the smallest non-zero p value in the data (or, say half the lowest p value). Then you end up distorting the plot for the points you can represent. I'd much rather just show a warning that there are points with p values of 0 that can't be shown- and the user can go find those in the tables. |
#232 solves this, closing this PR |
In response to #227
PR checklist
nf-core lint
).nextflow run . -profile test,docker --outdir <OUTDIR>
).docs/usage.md
is updated.docs/output.md
is updated.CHANGELOG.md
is updated.README.md
is updated (including new tool citations and authors/contributors).