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aertslab / SCENIC

SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.
http://scenic.aertslab.org
GNU General Public License v3.0
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Could not find function "plotTsne_rgb" #187

Closed AAA-3 closed 3 years ago

AAA-3 commented 3 years ago

Following the vignette:

Code: cellCol <- plotTsne_cell(scenicOptions, regulonNames, aucType="AUC", aucMaxContrast=0.6)

Error: 

Error in plotTsne_rgb(scenicOptions, regulonNames, aucType = "AUC", aucMaxContrast = 0.6) : 
  could not find function "plotTsne_rgb"

The command doesn't seem to exist... image @s-aibar could you advise?

jiangfuqing commented 3 years ago

Hi, I meet the same question, have you fixed it now?

AAA-3 commented 3 years ago

Nope - not sure how quite to address it - I came across the source code but when I copied that in it still wouldn't work. Try it anyway hopefully it works for you...

morganee261 commented 3 years ago

Hello, it seems like it was replaced by this function : plotEmb_rgb plotEmb_rgb(scenicOptions,regulonNames = regulonNames,aucType = "Binary",aucMaxContrast = 1,offColor = "lightgray",showLegend = F) this line works for me.

Morgane

AAA-3 commented 3 years ago

Hello, it seems like it was replaced by this function : plotEmb_rgb plotEmb_rgb(scenicOptions,regulonNames = regulonNames,aucType = "Binary",aucMaxContrast = 1,offColor = "lightgray",showLegend = F) this line works for me.

Morgane

Oh yep! Sorry I forgot to update the thread - yes, looks like the function is deprecated and replaced with plotEmb_rgb. The source code is found on GitHub but the vignette for Running Scenic is not updated for the 2021 release of the package.

Also, for me, I used SCENIC::plotEmb_rgb() because R would keep referring to AUCell package which has different inputs!