spatialdata-plot
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Static plotting for spatialdata
Hello, I need to plot the spatial locations of bins belonging to leiden clusters (one cluster per plot), but the color of each bin plotted should be colored based on...
Dear author, I use below command, but the cell type annotation is not working for colors: ``` sdata_crop1.pl.render_labels("cell_labels", color="Celltype", table_name='table2').pl.show(title="Cell labels", dpi=300, coordinate_systems="global") ``` Output figure contains no cell type...
Fix coloring of shapes, labels and points when there are nan values in the vectors to color by
As shown in this thread here: https://github.com/scverse/spatialdata-notebooks/pull/138, when using `imshow()` on very sparse matrices, the resulting plot can be misleading (the same problem appears also when plotting data using in...
The following code ```python import spatialdata_plot from spatialdata.datasets import blobs from spatialdata.transformations import Scale, set_transformation import matplotlib.pyplot as plt sdata = blobs() set_transformation( sdata["blobs_points"], transformation=Scale([1, 5], axes=("x", "y")), ) _,...
Hi, I work with spatialdata 0.3.0, and spatialdata_plot 0.2.9. When calling render_shapes() on Merfish data, with a color argument, plot fails with error: `ValueError: cannot insert EntityID, already exists`. This...
``` import os as os import glob import numpy as np import pandas as pd import scanpy as sc import anndata as ad import matplotlib.pyplot as plt import seaborn as...
`cookiecutter-scverse` released [v0.5.0](https://github.com/scverse/cookiecutter-scverse/releases/tag/v0.5.0). ## Changes ### New template sync We re-implemented template sync from scratch instead on relying on cruft. This allows us to create *real merge conflicts* that show...
When I try to plot expression values on my labeled images and plot the global coordinate system I am getting a colorbar foreach of my 25 labeled images. `sdata.pl.render_labels(color="log1p_total_counts", outline_alpha=0.9).pl.show(coordinate_systems='global',...
