Skip to main content
5 votes
Accepted

Running python script from terminal: umap issue

You answered your own question, yet it is not a coincidence that you have to change the name of your script. When Python executes your custom script, it reads: import umap Python will first ...
Kasper Thystrup Karstensen's user avatar
3 votes

umap and Louvain clustering on normalized data

If the data are single-cell RNA seq, after normalization can we do UMAP and Louvain clustering ? Typically people run PCA, UMAP and Louvain clustering on the normalised and log-transformed ...
Chris_Rands's user avatar
  • 3,948
2 votes

umap and Louvain clustering on normalized data

There is discussion if scaling the data (making the data range for all genes the same) is something you need for single cell data. The argument is that the expression differences between genes ...
PPK's user avatar
  • 886
2 votes

Adding certain barcodes to metadata in Seurat

If you want to add metadata to a Seurat object the new metadata needs to have the same length as the old metadata (== number of cells). For an example, if you have a 8 cells ...
PPK's user avatar
  • 886
2 votes
Accepted

umap failed to cluster the cells

Without more code and data, this can't be debugged. But first question would be does the data pass basic QC (e.g. look at cellranger web summaries or equivalent). If yes, you could trying different ...
Chris_Rands's user avatar
  • 3,948
1 vote

How to get started with louvain/leiden algorithm with UMAP in R

Both conda and PyPI have leiden clustering in Python which operates via iGraph ...
M__'s user avatar
  • 12.5k
1 vote

Using different "principal components" in UMAP visualizations

You can plot UMAP3 too in 3 dimensions, but that's about the limit for viz. You could plot UMAP2 vs. UMAP3, UMAP3 vs. UMAP4 etc. but I'm not sure how informative it is. Instead, you can focus on other ...
Chris_Rands's user avatar
  • 3,948
1 vote

umap highlighting two different models

By default, DimPlot colors the cells by their "identity class", stored in Ident(scData) in your case. This indeed contains the ...
milanmlft's user avatar
  • 151
1 vote
Accepted

RunUMAP in Seurat not working: module 'umap' has no attribute 'UMAP'

This is resolved by installing the more recent version of the code from GitHub. ...
Scott Gigante's user avatar

Only top scored, non community-wiki answers of a minimum length are eligible