Can we change marker genes used in scatter plots?

wguo-research / scCancer

A package for automated processing of single cell RNA-seq data in cancer

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Can we change marker genes used in scatter plots? #11

Closed dioncst closed 4 years ago

dioncst commented 4 years ago

Can we set personalized marker genes showed in part 3.1 Markers expression profile ?

wguo-research commented 4 years ago

Yes, you can input your interested genes to "runScAnnotation" function by the argument "show.features". Using help(runScAnnotation) can get more detailed information.

dioncst commented 4 years ago

Thank you for your quick reply. This is a really wonderful package. Also, I saw "cnv.ref.data" argument. I'm wondering how can we use our own normal reference data(10X)？ Can you give some examples?

wguo-research commented 4 years ago

The cnv.ref.data can be set as a count matrix of gene by cell. The row names are genes' symbol, and the column names are cells' label (such as "Normal1", "Normal2", etc). And cnv.referAdjMat can be set as NULL or a SNN matrix of reference data.