Squidpy 1.2.0 (2022-04-19)
Features
Add
squidpy.pl.spatial_scatter()
andsquidpy.pl.spatial_segment()
to statically plot spatial omics data. @giovp #437Add
squidpy.datasets.visium()
to download 10x Genomics datasets. @dineshpalli #449Add
squidpy.read.visium()
,squidpy.read.vizgen()
andsquidpy.read.nanostring()
to read Visium, Vizgen and Nanostring files, respectively. @dineshpalli #468An optional
ax
keyword can now be passed tosquidpy.pl.nhood_enrichment()
function. The keyword can be used to create a matplotlib figure outside of squidpy and then plot on any matplotlib subplot, which could give the user greater flexibility in working with enrichment plots. @jo-mueller #493Add option to load remote Zarr store in
squidpy.im.ImageContainer
. @ilan-gold #500Enable specifying diameter in
squidpy.im.ImageContainer.generate_spot_crops()
. @MxMstrmn #514Add
library_key
insquidpy.gr.spatial_neighbors()
to support building graphs across multiple slides. @giovp #516
Bugfixes
Fix source/target being
None
insquidpy.gr.ligrec()
. @michalk8 #434Do not set edge with in
napari
since it caused all points to be black. @michalk8 #488Fix
use_raw
insquidpy.gr.spatial_autocorr()
. @michalk8 #506Include check to be able to load ImageContainer that were generated from another version of squidpy. @MxMstrmn #508
Fix a typo when saving a figure caused a strange directory name to be created. @michalk8 #510