Unable to set vmin vmax when plotting vector data

Hi,
I want set the vmin and vmax of the color, but failed. This is the first method:

norm = matplotlib.colors.Normalize(vmin=-1.0, vmax=0.4)
sdata.pl.render_shapes("cell_circles", norm=norm, color="NOTCH2", method="matplotlib").pl.show(coordinate_systems= "physical", figsize=(10,4))

The resulting plot is here:

This is the second method:
sdata.pl.render_shapes("cell_circles", vmin=-1, vmax=1, color="NOTCH2", method="matplotlib").pl.show(coordinate_systems= "physical", figsize=(10,4))
The resulting plot is here:

vmin and vmax didn't work in both cases.

Hi, this is related to this #303, please try using clip=True.

@LucaMarconato

@LucaMarconato
vmin and max only works for pl.render_images, but don't work for pl.render_shapes. And, even for pl.render_images, there is no colorbar at all ! As you can see from the spatialdata xenium tutorial:

Here is my dataset, there is still no colorbar !

Thanks for the observation. I have changed the title to emphasize that the issue is also open for vector data (the linked issue is indeed for raster data).
Regarding the missing colorbar, I already reported the issue here: #304, so we can follow up there. The developer assigned to the issue is temporarily not available for the next 14 days because of a pressing deadline.

Running into the same problem with spatialdata-plot version 0.2.6.dev3+gffd4a1f where:

region.pl.render_shapes(
    "cell_boundaries", color = "CD3E", vmax = 11, clip=True).pl.show(title="CD3", coordinate_systems="global", ax=axes[1])

region.pl.render_shapes(
    "cell_boundaries", color = "CD3E", vmax = 11).pl.show(title="CD3", coordinate_systems="global", ax=axes[1])

and

norm = matplotlib.colors.Normalize(vmin=0.0, vmax=2000)
region.pl.render_shapes(
    "cell_boundaries", color = "CD3E", norm=norm, clip=True).pl.show(title="CD3", coordinate_systems="global", ax=axes[1])

do not alter the colorbar limits / shape shading. Is there any update on the best way to fix this?

@olivermccallion

@olivermccallion
Here is a workaround, spatialdata doesn't support vmin and vmax generally:
#304

@wangjiawen2013

Thanks @wangjiawen2013

I'm trying to achieve the same behaviour as your opening post, where you were looking to specify min and max values to the render_shapes() colorbar when the shapes are shaded by a particular feature -- not so worried about having a color bar for raster data / render_images(). #304 seems to be a work around for this second issue. Is there a solution/workaround for the first?

Unfortunately not. #304 (comment)

@timtreis

@timtreis @olivermccallion
I have tested the latest spatialdata-plot (v0.2.6)
vmin and vmax works only in pl.render_images, but still don't work in pl.render_shapes .

As you can see, vmin and vmax changed the min and max number on the colorbar, but the color in the figures was not changed at all ! It is expected to be more brighter when decreasing vmax, which is the case in pl.render_images.

@wangjiawen2013

Hey @wangjiawen2013,

if I understand correctly, this is your usecase?

Or did I misunderstand something?

The current norm based approach allows you to make use of the other mpl.colors Normalisation methods, like f.e. this:

@timtreis

@timtreis
Yes, this is what I mean ! I am not familiar with matplotlib norm and don't know the clip parameter. I tested my data and found this works in pl.render_images, while don't work for pl.render_shapes, could you extend norm to pl.render_shapes` ?

Oh weird, I'd think it should also work for render_shapes. I'll investigate and ping you

Picking this up today as my first PR getting back to development hehe. Will report back

I take it that we should perhaps also add a notebook explaining the matplotlib norm.

Agree. We can add this to the static plot workshop notebook and maybe a few extra notebooks in the spatialdata repo.

ok fixed it, just testing now, but here already with vmin / vmax / clip and without:

@wangjiawen2013

@wangjiawen2013 if you would like you can check #368 to see whether it fixes the issue for you. This only fixes it for the matplotlib render. Once the solution is in I will also create a fix for the datashader.

@melonora

@melonora
Hi,
I am trying to test it. Is this fixes released in current spatialplot version ?

Hi! This is not in the current release yet I believe. Thanks for your willingness to test! If you want you can test from main.

@wangjiawen2013

Hey @wangjiawen2013, it's not yet released but we'll have one this week that also includes a bunch of datashader fixes :)

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Unable to set vmin vmax when plotting vector data #324

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Unable to set vmin vmax when plotting vector data #324

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LucaMarconato commented on Aug 16, 2024

wangjiawen2013 commented on Aug 17, 2024

LucaMarconato commented on Aug 19, 2024

olivermccallion commented on Sep 1, 2024

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