DotPlot : Plot markers per Cluster - Gene Expression & n° of Cells expressing the marker

[matteozoia4]

Dear all,

I would like to retrieve for several gene-markers their expression and % of cells expressing it, this per each cluster.
I would need a DotPlot-like figure, how could I approach this representation?

Should I use GeneScore or GeneExpression matrix?
And more importantly, is it possible to apply DotPlot format?

Many thanks for your advices,

MZ

[rcorces]

ArchR does not provide infrastructure for this. Certainly GeneScoreMatrix cannot be accurately used for this. You will have to obtain whatever data you are interested in from ArchR, likely using getMatrixFromProject() or exportGroupSE() and perform your manipulations and plotting on your own

[matteozoia4]

Many thanks! Matteo Zoia, Ph.D. Student Gene Regulation & Cardiac Development Osterwalder Lab Department for BioMedical Research (DBMR) University of Bern Murtenstrasse 28, 369 CH - 3008 Bern SWITZERLAND

…

________________________________ Da: Ryan Corces ***@***.***> Inviato: lunedì, 21. novembre 2022 15:30:22 A: GreenleafLab/ArchR Cc: Zoia, Matteo (DBMR); Author Oggetto: Re: [GreenleafLab/ArchR] DotPlot : Plot markers per Cluster - Gene Expression & n° of Cells expressing the marker (Discussion #1749) ArchR does not provide infrastructure for this. Certainly GeneScoreMatrix cannot be accurately used for this. You will have to obtain whatever data you are interested in from ArchR, likely using getMatrixFromProject() or exportGroupSE() and perform your manipulations and plotting on your own — Reply to this email directly, view it on GitHub<#1749 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AUBHT3AUKKOZLRFMUN5DAYTWJOBP5ANCNFSM6AAAAAASGSHCVQ>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[Zepeng-Mu]

#882