chansigit / hitl-single-cell

Human-in-the-loop Single-cell Analysis

Human-in-the-loop Single-cell Analysis

Manual cell selection

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Manual selection of data is actually very important for single-cell analysis.

Here we show how cells can be selected with interactive widgets in Jupyter.

import jscatter
lst = interactive_scatter_list(adata, 
                         var_list=['Cd3d','ann220413' ], 
                         embedding_list=['X_umap-t4.0-L1.0','X_umap-t4.0-L1.0'])

jscatter.link(lst, rows=1)

# get selected cells
cell_number_1  = lst[0].selection()
cell_indices_1 = adata.obs_names[cell_number_1]
print("# of selected cells", len(cell_indices_1))

integration pipeline

TODO