spatialdata-plot

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Q: How to render xenium morphology image with original colors?

15

Hello @LucaMarconato! Thank you very much for this tool. I want to plot a part of morphology image acquired with xenium + multimodal segmentation kit. It is loaded into spatialdata...

tsvvas

[pre-commit.ci] pre-commit autoupdate

1

updates: - [github.com/astral-sh/ruff-pre-commit: v0.6.4 → v0.6.9](https://github.com/astral-sh/ruff-pre-commit/compare/v0.6.4...v0.6.9)

pre-commit-ci[bot]

Categorical color obs column crashes the plotting

2

Hi, When the "color" is categorical, it crashes and returns ValueError in version 0.2.6. The categorial "test" column contains NaN values. There are 11 possible categories. This code was working...

sinanugur

Using groups in pl.render_shapes() fails with large data

1

Hello, I work with **spatialdata-plot version: 0.2.7.dev2+g6ffe22b** on the following visium HD data:  I have annotated the 8um bins table with cell clusters:  When I do a subset...

ConstensouxAlexis

Datashader shapes outlines and fill_alpha documentation

7

Status after #309, just to document some thoughts/details about the comparison between ds and mpl: 1. outlines linewidth with datashader seems to vary slightly between e.g. polygons and circles, which...

Sonja-Stockhaus

Refactoring of colorbar logic

2

Before  After 

timtreis

'SpatialData' object has no attribute 'pp'

2

Hello, I am attempting to follow the 10x Visium example notebook (https://spatialdata.scverse.org/en/latest/tutorials/notebooks/notebooks/examples/technology_visium.html#technology-focus-10x-genomics-visium) and are encountering issues when attempting to colour the visium spots by gene expression. Running: ```python ( visium_sdata.pp.get_elements("ST8059050")...

lg907

 This is expected but might be surprising to a user. We should include this information in the warning.

timtreis

Points not transformed when `method="datashader"`

3

As per the title, I just ran into a case where `datashader` was chosen as the method for `render_points`, which led to my points being plotted without the relevant transformation...

clwgg

When multiple categories are plotted, only one legend is shown, and colors do not match

3

Plotting a single categorical variable works great. This code plots two categorical variables together. Problems: - [ ] The legend gets mixed; I would consider adding two legends. - [...

LucaMarconato