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 ...
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 ...
- 3,858
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 ...
- 858
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 ...
- 858
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 ...
- 3,858
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__♦
- 10.2k
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 ...
- 3,858
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 ...
- 153
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.
...
- 2,123
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