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rezakj / iCellR

Single (i) Cell R package (iCellR) is an interactive R package to work with high-throughput single cell sequencing technologies (i.e scRNA-seq, scVDJ-seq, scATAC-seq, CITE-Seq and Spatial Transcriptomics (ST)).
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Ploting colonotypes #20

Closed crushseven-7 closed 4 years ago

crushseven-7 commented 4 years ago

Hi there, I am tring to use these package to analysis my scTCR data. When I try to plot colonotypes, I am quite confused about the clono paremeters in clono.plot function. This parameter seems only recepted number rather than raw_clonotype_id in vdj data. I am curious about how can I pre-define this clonotype name. Best, Yan

rezakj commented 4 years ago

Hi Yan,

Yes yes, thanks for reminding, I will need to fix a few things for that function. Will update you today and update the tutorial and let you know.

Reza

crushseven-7 commented 4 years ago

Thank you for your quick response. I am really looking forword to it :)

rezakj commented 4 years ago

First update iCellR to version 1.5.8. It's not in CRAN yet so update from GitHub.

Then add your VDJ data to iCellR object my.obj <- add.vdj(my.obj, vdj.data = my.vdj.data)

The rest is explained in detail in the updated section for plotting "How to plot clonotypes".

crushseven-7 commented 4 years ago

awsome! I tried my data just now, it could not only select the colontype id, even any column in the contig file could be selected to plot. Appreciate for your excellent work.