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sdata.pl.render_points() works weird #320

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sdata.pl.render_points() works weird#320

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@wangjiawen2013
wangjiawen2013
opened on Aug 13, 2024

Hi,
I find sdata.pl.render_points() works wiered when using the default datashader method. Maybe there there something wrong when processing the coordinates for datashader.
The output of sdata.pl.render_points("transcripts", color="feature_name", groups="A2M", size=100, palette="orange").pl.show():
image

The output of sdata.pl.render_shapes("cell_boundaries", color="A2M").pl.render_points("transcripts", color="feature_name", groups="A2M", size=100, palette="orange").pl.show() is similiar, the coordinate of transcripts is global:
image

The output of sdata.pl.render_shapes("cell_boundaries", color="A2M").pl.render_points("transcripts", color="feature_name", groups="A2M", method="matplotlib", palette="orange").pl.show() worked well:
image

Here is my spatialdata object:
image

Activity

  1. LucaMarconato commented on Aug 13, 2024

    @LucaMarconato
    LucaMarconato
    on Aug 13, 2024
    Member

    Thanks for the details. You are correct, there is problem with datashader which I reported here #291 and is currently being worked on. In the issue I posted a workaround (transform the points data before plotting).

    Regarding the axis name, we do not plan to automatically write spatial; but if you are interested it you can for instance do

    import matplotlib.pyplot as plt

plt.figure()
ax = plt.gca()
sdata.pl.render_shapes(...).pl.show(ax=ax)
ax.set_xlabel('X-axis label')
ax.set_ylabel('Y-axis label')
plt.show()

    Closing the issue as duplicate of #291.

  2. LucaMarconato
    closed this as completedon Aug 13, 2024

  3. LucaMarconato commented on Aug 13, 2024

    @LucaMarconato
    LucaMarconato
    on Aug 13, 2024
    Member

    CC @timtreis

  4. timtreis
    changed the title [-]sdata.pl.render_points() works wiered[/-] [+]sdata.pl.render_points() works weird[/+] on Aug 26, 2024
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