I'm trying to show cell cycle regression and input sample metadata to my umap.

I've been following Satija Lab's tutorials and have generated my umap but now want to specify which sample corresponds to each cluster, if one sample is driving a certain cluster, etc. I also, would like yo show cell cycle regression in each cluster. I following the cell cycle regression tutorial but that only tells me the board overview of the cells in each cycle. I would want to highlight it in the umap.

How would I go about each of these tasks?


You can use the group.by argument of the DimPlot() function. group.by accepts column names present in the meta.data column of the Seurat objects.

  • $\begingroup$ How do I add the sample and cell cycle regression information to the metadata? $\endgroup$
    – mmpp
    Feb 5 '20 at 17:26
  • $\begingroup$ Seurat::CellCycleScoring() stores the cell cycle information in the meta.data slot. Sample information can be added with Seurat::AddMetaData(). $\endgroup$
    – haci
    Feb 5 '20 at 19:33
  • $\begingroup$ The other useful line for DimPlot (or FeaturePlot) is "split.by", which will make separate plots for each sample or whatever all side by side. $\endgroup$
    – swbarnes2
    Jul 3 '20 at 21:39

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