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Run UMAP with specific dimension in Velocyto using Seurat #28

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sikh09 opened this issue Feb 10, 2020 · 0 comments
Open

Run UMAP with specific dimension in Velocyto using Seurat #28

sikh09 opened this issue Feb 10, 2020 · 0 comments

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@sikh09
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sikh09 commented Feb 10, 2020

Hi
I have a plot after running Velocyto using Seurat.
Filtered_cells_S1_velocyto_dim20.pdf
I want to zoom into the upper clusters, where the dimensions are following UMAP_1 >-5 and UMAP_2 >5.
I tried to save these dimensions like this way.

umap <- data.frame(bm@reductions$umap@cell.embeddings, row.names = rownames(bm@reductions$umap@cell.embeddings)

Could you plz tell me how can I plot only a specific dimension in Velocyto?
Thanks

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