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wenweixiong / MARVEL

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Plotting error for SJ position for droplet dataset #40

Open nehagupta1215 opened 1 month ago

nehagupta1215 commented 1 month ago

Hello Wei, Running the MARVEL package using the droplet method on the data provided by the package. Getting this error for Locate SJ Position foradhocGene.PlotSJPosition.10xcommand.

marvel <- adhocGene.PlotSJPosition.10x(MarvelObject=marvel,
                                           coord.intron=coord.intron,
                                           rescale_introns=FALSE,
                                           show.protein.coding.only=TRUE,
                                           anno.label.size=1.5,
                                           anno.colors = c("black", "red", "blue")
                                           )
Retrieving transcripts from GTF file...
11 transcripts identified
Error in wiggleplotr::plotTranscripts(exons = grange.exon.list, cdss = grange.cds.list,  : 
  unused arguments (anno.colors = anno.colors, anno.label.size = anno.label.size)

Looked into the wiggleplotr::plotTranscripts function and it looks like it does not takeanno.colors amd anno.label.sizearguments. Is this something you guys came across as well? If so, any idea how to get a way around this. Running on Ubuntu OS. Thanks!!

wenweixiong commented 1 month ago

Please may you install the customised wiggleplotr R package. Simply refer to "Install adjunct customised package" section of the MARVEL Github page: https://github.com/wenweixiong/MARVEL