Comments (7)
Does the refactor of the scatterplot module include moving the code for spatial plotting out of sc.pl.embedding
?
from squidpy.
Not sure what's @flying-sheep opinion on this. So far, pl.spatial
is essentially a wrapper of sc.pl.embedding
with a couple of additions:
- function to process images and plot them
- use of "circles" (from PatchCollection) instead of "scatter"
from squidpy.
Yeah, we added a bit more to what’s already too many options. No idea how to nicely deprecate and replace it by something better, and that didn’t change by those additions.
I think the best would be to extract the image-below-things to sc.pl.spatial
, but leave the option to do circles instead of markers.
from squidpy.
I don't think those options have been documented in a release. Can we just not document them for the regular embedding functions?
Really, a lot of those plotting functions could be more modular.
from squidpy.
Yeah. If nobody picks up the slack until I’m done with my thesis, I’ll do it after. But it’s really a thing we need.
from squidpy.
Could we make sure that those arguments don't get documented in a release? Also, I think the doc builds have been broken since the wishbone PR. It might be worth asking read the docs to enable doc builds for our PRs.
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closed with #437
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Related Issues (20)
- Using squidpy.pl.spatial_segment on Xenium data
- The Kernel crashed while executing code in the current cell HOT 1
- Ripley L measure with n_observations
- add zarr.zip to adata HOT 1
- KeyError: '72' when reading in Nanostring CosMx data HOT 4
- Converting spatial seurat dataset to anndata HOT 2
- Should the raw H&E image (.tif) and the image stored in anndata be in the same orientation? HOT 1
- sq.gr.ligrec crashing kernel/script with VisiumHD (>100k spots/spatial barcodes) - Squidpy incompatible with single-cell level spatial technologies? HOT 3
- Extracted cropped spot images HOT 1
- Clustering according to image features
- sort_order for pl.spatial_scatter
- Stacking XYZ dimension images of mouse brain into 3D Volume
- `calculate_image_features()` error with tutorial data HOT 1
- matplotlib update leads to import error HOT 8
- Sliding window across spatial neighbourhood HOT 2
- When attempting to install, dependency "pygeos" gives: module 'configparser' has no attribute 'SafeConfigParser' HOT 1
- neigh_correct when computing spatial graph
- Vizgen-MERFISH multiple dataset integration/comparison
- `var_by_distance` using polygons annotations
- build spatial neighbors graph with spatialdata elements
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