squidpy
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Spatial Single Cell Analysis in Python
Hi, Does sq.pl.ligrec support plots similar to cellphoneDB ? Because when there are many clusters, the interaction plot generated will be very large and hard to save and to see....
Hi, I am currently learning Squidpy calculate image features. I am wondering what is the interpretation of the pattern? I could not figure out why there are circles of low-mean...
Hello, I am trying to read in multiomic data from the newly released 10X open source datasets: https://www.10xgenomics.com/resources/datasets/multiomic-integration-neuroscience-application-note-visium-for-ffpe-plus-immunofluorescence-alzheimers-disease-mouse-model-brain-coronal-sections-from-one-hemisphere-over-a-time-course-1-standard This dataset is not included in the sample_ids within sq.datasets.visium. It has...
When running `sq.gr.nhood_enrichment` function, I got the warning below: ``` 100%|██████████| 1000/1000 [00:00
Hi, when I ran sq.gr.co_occurrence, it used all the 128 cores of my server, even the n_jobs were set to n_jobs=30, how to limit the number of cores it uses...
Hi, Each time I use sq.gr.ligrec() to perform receptor-ligand analysis, squidpy will re-download the interaction database. sometimes it takes a long time to download because of the poor internet. So...
Hi All, When using the `sq.pl.nhood_enrichment` function we obtain a heatmap with certain scale - what do the values represent? can one obtain statistical significance of the results? Thanks!
If I use matplotlib 3.5.2, I will receive this bug: [Matplotlib AttributeError: module 'matplotlib.cbook' has no attribute '_define_aliases'](https://stackoverflow.com/questions/53421905/matplotlib-attributeerror-module-matplotlib-cbook-has-no-attribute-define-a) If I use 3.5.0, the package can work normally. How to address...
Hi, I don't quite understand about the "library_key" parameter in sq.gr.spatial_neighbors. I have integrated several datasets in an anndata object, the datasets are from different 10xvisium samples. In this case,...
text from zulip from phil https://results.pre-commit.ci/. The link there e.g. leads to https://github.com/apps/pre-commit-ci/installations/23763214
