Unable to set vmin vmax when plotting vector data

[wangjiawen2013]

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.

[LucaMarconato]

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

[wangjiawen2013]

@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 !

[LucaMarconato]

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.

[olivermccallion]

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?

[wangjiawen2013]

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

[olivermccallion]

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?

[wangjiawen2013]

Unfortunately not. #304 (comment)

[wangjiawen2013]

@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.