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Add "sort_by" in rank_genes_groups

1

- [x] Additional function parameters / changed functionality / changed defaults? - [ ] New analysis tool: A simple analysis tool you have been using and are missing in `sc.tools`?...

zhangnan0107

filter_rank_genes_groups fold change calculation

9

`filter_rank_genes_groups` handles log values differently than the `rank_genes_groups` function. The discrepancy gives different DE gene lists when filtering genes based on `log2fc_min=1` with `get.rank_genes_groups_df` vs `min_fold_change=2` with `tl.filter_rank_genes_groups` In rank_genes_groups,...

coh-racng

show the mean of several genes in spatial scanpy figure

4

... Hello I would like to plot the "log1p_total_counts" of a **visium transcriptomic dataset** (AnnData object with n_obs × n_vars) using sc.pl.spatial **sc.pl.spatial(adatal, img_key="hires", color=["gene1", "gene2", "gene3"]) -**-> gives 3...

sophieRAIBAUD

Dotplot color annotation

7

- [ x] Additional function parameters / changed functionality / changed defaults? - [ ] New analysis tool: A simple analysis tool you have been using and are missing in...

Hrovatin

ValueError at sc.pp.highly_variable_genes() using seurat_v3 flavor.

1

- [x] I have checked that this issue has not already been reported. - [x] I have confirmed this bug exists on the latest version of scanpy. - [ ]...

lijinbio

Illegal slicing argument for scalar dataspace when attempting to read 10x_h5 with version 1.9.0

4

Hi When attempting so simply read a h5 file with: ``` Python version - 3.8.8 # results_file = path to 10X h5 file # adata = sc.read_10x_h5(results_file) ``` I get...

nadavyayon

UMAP transform

9

- [ x] Additional function parameters / changed functionality / changed defaults? - [ ] New analysis tool: A simple analysis tool you have been using and are missing in...

Hrovatin

Idents in Featureplot in Seurat outputs Idents name on top of the if Label is set to true. How do we see labels on top of scanpy UMAP plots.

6

Hi, Seurat allows us to set an Ident and when we do a feature plot we can label that feature plot with that ident. If I were to achieve something...

smk5g5

"dot_color_df" is currently not documented for https://scanpy.readthedocs.io/en/stable/generated/scanpy.pl.dotplot.html#scanpy.pl.dotplot CC @fidelram

Zethson

read_10x_mtx with different prefix

10

Hi scanpy team, I am not sure if I just missed it, but there does not seem to be a way to specify a different filename for ``.mtx`` files. For...

alexblaessle