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kstreet13 / slingshot

Functions for identifying and characterizing continuous developmental trajectories in single-cell data.
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plotGenePseudotime was removed from current version #155

Closed FADHLyemen closed 2 years ago

FADHLyemen commented 2 years ago

Hi plotGenePseudotime was removed? https://github.com/kstreet13/slingshot/blob/master/NEWS.md

what is alternative function to use?

kstreet13 commented 2 years ago

Yes, we decided to make a separate visualization package, traviz, in order to ease the dependency requirements of slingshot, tradeSeq, and condiments. The recommended alternative is traviz::plotSmoothers.

FADHLyemen commented 2 years ago

Thank you, could plotSmoothers plot per lineage in separated plot

FADHLyemen commented 2 years ago

I tried p=plotSmoothers(sce_PT, assays(sce_PT)$counts, gene = "SLC5A2", alpha = 1, border = TRUE) + ggtitle("SLC5A2") p+facet_wrap(lineage~,scale='free')

but does not work

kstreet13 commented 2 years ago

I am not a ggplot expert, so I don't know if this is possible. I would recommend asking in the traviz package.

I would personally pull out the relevant pieces (eg. assays(sce_PT)$counts["SLC5A2",] and sce_PT$slingPseudotime_1) and then plot them with a loess smoother, which is essentially what the plotGenePseudotime function did.