Slide-seq

import warnings
warnings.filterwarnings("ignore")

import SOView
import scanpy as sc

scanpy==1.9.1 anndata==0.8.0 umap==0.5.2 numpy==1.22.4 scipy==1.7.3 pandas==1.5.3 scikit-learn==1.0.2 statsmodels==0.13.5 python-igraph==0.10.4 pynndescent==0.5.8
squidpy==1.1.2

adata_raw =sc.read_h5ad('/data/linsenlin/binary/binary1/Slide-seq/BINARY_Slide-seq(knn23).h5ad')

adata = adata_raw.copy()

sc.pp.neighbors(adata,use_rep='BINARY')

sc.tl.umap(adata,n_components=3)

adata.obsm['X_umap'].shape

(53208, 3)

SOView.SOViewer_plot(
    adata = adata, # the data to plot
    save = f'Slide-seq', # save the result to specified path or don't save (None)
    embedding_use='X_umap', # which embedding to be used for plot
    dot_size=1, # the marker size of the plot
)

generating color coding...
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