squidpy

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Pass/Retrieve matplotlib ax instance to/from plots

10

## Description Follow-up feature to #481 - I think it could be nice for plotting to add a matplotlib ax keyword to all built-in plot functions which would allow passing...

jo-mueller

Napari visualization of AnnData Visium containing only a single library is broken

4

Following the documentation and tutorials, code like ``` image = sq.im.ImageContainer(adata.uns["spatial"]["spaceranger100_count_30458_ST8059048_mm10-3_0_0_premrna"]["images"]["hires"], scale=adata.uns["spatial"]["spaceranger100_count_30458_ST8059048_mm10-3_0_0_premrna"]["scalefactors"]["tissue_hires_scalef"]) viewer = image.interactive(adata) ``` should work and has worked in the past. However, with Squidpy 1.2.0, it aborts...

ilia-kats

get_axis() for pl.ligrec

1

## Description ... Thanks everyone for developing Squidpy. I just had a small request/question regarding plotting ligrec. After plotting ligrec dotplots, I usually want to see whether ligand or receptor...

Tonyspuri

how to get the result from each permutation in gr.ligrec

3

Hi there, I am trying to get the result from each permutation in gr.ligrec, which is the mean expression of the ligand receptor pair in all interaction clusters. I thought...

K10308

Nhood composition comparison across conditions?

5

Hello! I work with CODEX data across different conditions and I was wondering whether there is a way to visualise/summarise the differences in neighbourhood composition across the different conditions, after...

annamath

conda-forge package

4

It would be great if this package could be distributed via condo-forge as well as pip. I'd like for `mamba install squidpy` to work so the package doesn't have to...

ivirshup

Variable grouping to `squidpy.pl.ligrec`

2

## Description (This is a suggestion/request; love the software) The dotplots output by `squidpy.pl.ligrec` are beautiful, but sometimes the number of ligand-receptor interactions can get unwieldy, and are not sorted...

dnjst

`sc.pl.spatial` alpha values for continuos/discrete annotations

6

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

giovp

apply image rotation when plotting tissue / cellxgene

1

## Imege rotation Hi, when plotting cell position on top of images (sc.pl.spatial) would it be possible to apply a predefined rotation to it? This could either be an argument...

mkunst23

Default color of segmentation masks

1

Hi, May i know what the color represents in the segmentation image on the right ?  Thanks

raman91