MERSCOPE

import warnings
warnings.filterwarnings("ignore")

import SOView
import scanpy as sc

adata_raw =sc.read_h5ad('/data/linsenlin/binary/binary1/MERSCOPE/R1S2_knn15.h5ad')

adata = adata_raw.copy()

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

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

adata.obsm['X_umap'].shape

(83546, 3)

SOView.SOViewer_plot(
    adata = adata, # the data to plot
    save = f'R1S2', # 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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