Closed DaianeH closed 1 year ago
Just adding, seurat object was converted to ann file in R with:
library(Seurat) library(SeuratDisk) seurat.d7<- readRDS(file = "(seurat.d7.rds") SaveH5Seurat(seurat.d7, filename = "seurat.d7.h5Seurat") Convert("seurat.d7.h5Seurat", dest = "h5ad")
Also adding:
When I plot my adata BEFORE merging with the loom matrix, the UMAP plot looks like what I expect. The problem happens after merging with the loom. What can be wrong with the loom, or with the merging process?
Hi, I'm new to scRNA-seq analysis with Python, so following the tutorial example in: https://uci-genpals.github.io/pseudotime/2021/02/09/scvelo-tutorial.html
My exact commands were:
The UMAP plot I get however looks like something I've never seen:
umap_celltypes.pdf
When I further try to compute trajectories and plot them with:
I get the error:
"ValueError: Expected n_neighbors > 0. Got 0"
What can be causing this problem? Could it be a problem with my files? I don't have experience with scRNA-seq analysis in Python, so this is what the merged dataset looks like:
Any help is greatly appreciated.
Versions
```pytb scvelo==0.2.4 scanpy==1.7.2 anndata==0.7.8 loompy==3.0.7 numpy==1.19.5 scipy==1.5.4 matplotlib==3.3.4 sklearn==0.24.2 pandas==1.1.5 ```