Timeline for how to change the PC use in the dimplot and feature plot
Current License: CC BY-SA 4.0
6 events
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| Dec 20, 2019 at 19:03 | comment | added | Kohl Kinning |
If I understand your question correctly, replace reduction = "pca" with reduction = "umap". You'll also have to keep more dims when you do RunUMAP(), the default is to keep two. Be sure to add dims.keep = 5L to RunUMAP() if you want to access dims 4 and 5. If you need any more detail, you should ask another question as this has branch from your original question and would be more helpful for future seekers if it were on it's own.
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| Dec 20, 2019 at 1:00 | comment | added | hua | Hi Kohl, thank you for your advice. And I have successfully got the PC change, but I would like to know whether we can change the UMPA use? like the PC use? | |
| Dec 19, 2019 at 21:57 | comment | added | Kohl Kinning |
From the docs: **reduction** Which dimensionality reduction to use. If not specified, first searches for umap, then tsne, then pca. I imagine you haven't run UMAP or tSNE yet. Try providing the reduction arg, I've updated my answer.
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| Dec 19, 2019 at 21:55 | history | edited | Kohl Kinning | CC BY-SA 4.0 |
add another arg for consistency
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| Dec 19, 2019 at 1:42 | comment | added | hua | Hi Kohl, thank you for your advice. But after I tried that code, I got the error:"Error in Embeddings(object = object[[reduction]])[cells, dims] : subscript out of bounds Calls: DimPlot Execution halted" Do you have any idea about this? | |
| Dec 18, 2019 at 22:26 | history | answered | Kohl Kinning | CC BY-SA 4.0 |