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UCLouvain-CBIO / scp

Single cell proteomics data processing
https://uclouvain-cbio.github.io/scp/index.html
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Scplainer #50

Closed cvanderaa closed 4 months ago

lgatto commented 6 months ago

I think there's a small bug in scpVariancePlot() - when using an fcol argument, the decreasing seems to be ignored. See the woo scplainer vignette for an example - the peptides aren't ordered by decreasing variance any more when labelling them by gene name.

cvanderaa commented 5 months ago

I think there's a small bug in scpVariancePlot() - when using an fcol argument, the decreasing seems to be ignored. See the woo scplainer vignette for an example - the peptides aren't ordered by decreasing variance any more when labelling them by gene name.

Actually, the decreasing is only intended for selecting the peptides to show. When fcol is provided, I use ggplot's facetting to group the peptides and each group (let's say protein) is automatically ordered alphabetically. Do you want me to change this behaviour? If so, how would you order the proteins? By the average value within the protein?