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snakemake-workflows / rna-seq-kallisto-sleuth

A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.
MIT License
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Interactive volcano plots #45

Closed tedil closed 3 years ago

tedil commented 3 years ago

This PR adds interactive volcano plots. This allows displaying hover information such as gene symbols, qvalue, pvalue, signed pi value, transcript. It also uses q-values on the y-axis instead of p-values. Circle size scales with standard error of the beta value of the covariate. I tried using error bars, but that looks really weird if you have a lot of points.

tedil commented 3 years ago

The volcano plots from sleuth really seem to be for QC only, since those use beta values vs qval per covariate, but not for the whole model. For the interactive plots, we want the whole model. We can stick with the last changes I made and use those instead of the sleuth ones for QC, but additionally provide the whole-model volcano plot in a different (sub)category in the snakemake report. Also @fxwiegand has been so kind as to translate the plots to vega-lite, so we might as well use those (the only qualm I have with those is that vega's hover tooltips are somewhat hard to trigger).

dlaehnemann commented 3 years ago

Yes, exactly. Thanks for keeping at this, even though I am so slow to respond during my parental leave.

I like the idea of replacing the sleuth plots, especially if it is with vega-lite plots (thanks @fxwiegand). This will make them so much more configurable in case we or collaborators want to twiddle some more.

And for the results, we definitely want the whole model qval volcano plots.