Questions tagged [umap]

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4 votes
2 answers
123 views

Question about umap using different numbers of pca components as initialization

I am new to the scRNA-seq field and I have been doing some experiments of visualization of UMAP using different numbers of PCA components for initialization. The process involves projecting scRNA-seq ...
0 votes
1 answer
202 views

How to analyze hashtagged data with scanpy?

I used hashsolo to demultiplex my data and I am a bit confused as to how to continue the analysis. Following hashsolo my samples look like below: ...
1 vote
0 answers
402 views

How to plot average gene expression in scanpy?

I would like to make a UMAP where the cells are colored by the average expression of the bulk signature genes but I am not confident that I did it correctly. I would like to use scanpy for it. I did ...
2 votes
0 answers
173 views

How to make a UMAP for single cell data and color cells by average expression of a list of genes in scanpy?

I would like to make a UMAP where the cells are colored by the average expression of the bulk signature genes but I am not confident that I did it correctly. I would like to use scanpy for it. I did ...
1 vote
1 answer
138 views

umap failed to cluster the cells

I tried umap visualization with scanpy : ...
1 vote
1 answer
403 views

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

A collegue of mine recently suggested to try the louvain algorithm for clustering multiplex cytometry data. However, implementations of louvain are kind of rare in R. To my knowledge the only stand-...
0 votes
1 answer
305 views

Using different "principal components" in UMAP visualizations

In certain UMAP visualization, it appears that the visualizations show the first UMAP "principal component" plotted against the second. For example, like this: Apparently, this lets us use ...
1 vote
0 answers
118 views

Different colors in UMAP

I have integrated top ten TCR clones into Seurat object something like below You are seeing some clones are expressed in more than one cells So in Seurat I have something like ...
0 votes
0 answers
3k views

DimPlot - How to highlight cells with identity colors?

I made this wrapper for DimPlot: ...
2 votes
3 answers
1k views

umap and Louvain clustering on normalized data

I know that scaled data must be used for PCA for example as it is based on variance maximization. However I'm wondering if it's the same case for UMAP ? If the data are single-cell RNA seq, after ...
1 vote
1 answer
77 views

Is there a difference between any scRNA-seq visualization and pseudotime?

Is there a good definition of pseudotime? Some tools are clearly labeled as pseudotime and produce values along a trajectory, but there are more complex approaches that involve branching and ...
1 vote
1 answer
162 views

umap highlighting two different models

I'm trying to create a umap for single cell data from human samples and ptx samples. I can get the umap to where it shows the umap with the different clusters but I want to show where the ptx samples ...
0 votes
2 answers
3k views

Adding certain barcodes to metadata in Seurat

I want to upload an excel file sheet that has certain barcodes that I would like to show on my umap. How do I go about adding the file and linking it to the metadata? Below is my following code. <...
0 votes
2 answers
601 views

Running python script from terminal: umap issue

Some time ago I asked the question: RunUMAP in Seurat not working: module 'umap' has no attribute 'UMAP' It was solved by following the answer in it, however, it is still not ...
3 votes
1 answer
4k views

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

I am trying to run UMAP in the following way: ...