spatialdata-plot

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Currently with the cosmx notebook I noticed in the example that when trying to only plot the outline by setting `outline` to True and `fill_alpha` to 0 no labels are...

melonora

Can't plot different elements in a specific axes when multiple coordinate systems are available

1

# Intro The bug that I'll describe is a consequence of the current coordinate systems implementation and will disappear when it will be refactored. The bug needs to be fixed...

LucaMarconato

Pixel shift in `render_images`

2

Hello, When plotting an image, it seems that there is a 0.5-pixel shift. This is not visible for large images but becomes very visible if we zoom in, and, mostly,...

quentinblampey

`pl.show()` still not working (?) in interactive mode

3

I am using the latest code from main. If I run this code as a script, the plot is shown. If I set a breakpoint (I am using PyCharm) in...

LucaMarconato

Hi all, I was wondering about the API design of spatialdata-plot: Why did you decide for requiring a `pl` before every plotting command in a "plotting pipeline", e.g. ```python sdata.pl.render_images().pl.render_shapes(color="KRAS").pl.show("downscaled_hires")...

grst

Hello, When rendering shapes, I get an error when trying to color shapes by a column of dtype `object` (containing strings) instead of dtype `category`. It would be great to...

quentinblampey

Plotting color instead of by var in table and alpha not respected

2

In the aggregation notebook in `spatialdata-notebooks` we color shapes at some point by aggregated points of gene `b`. However, it seems `b` is interpreted as color blue and the values...

melonora

Use spaco for picking colors?

4

Without having tried it yet, the figure looks convincingly nice. Basically calculates the degree of mixture of all cell type pairs and then maximises contrast based on the given palette....

timtreis

tbd @Sonja-Stockhaus @LucaMarconato

timtreis

Multiscale images lose channel names

1

Rendering commands that take channels fail when you pass channel names instead of indices. ## Example ```python from spatialdata import SpatialData from spatialdata.models import Image2DModel import numpy as np import...

aeisenbarth