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scverse / scirpy

A scanpy extension to analyse single-cell TCR and BCR data.
https://scirpy.scverse.org/en/latest/
BSD 3-Clause "New" or "Revised" License
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ir.pl.clonotype_network #531

Closed 1w2y3x6078 closed 2 months ago

1w2y3x6078 commented 3 months ago

mdata MuData object with n_obs × n_vars = 40797 × 25566 obs: 'sample', 'stim', 'cluster' uns: 'stim_colors', 'sample_colors' 2 modalities gex: 40359 x 25566 obs: 'sample', 'stim', 'cluster' var: 'gene_ids', 'feature_types' uns: 'log1p', 'pca', 'neighbors', 'umap', 'airr:chain_pairing_colors', 'airr:clonal_expansion_colors', 'airr:receptor_type_colors' obsm: 'X_pca', 'X_umap' varm: 'PCs' obsp: 'distances', 'connectivities' airr: 16772 x 0 obs: 'receptor_type', 'receptor_subtype', 'chain_pairing', 'clone_id', 'clone_id_size', 'clonal_expansion' uns: 'scirpy_version', 'chain_indices', 'ir_dist_nt_identity', 'clone_id', 'ir_dist_aa_alignment', 'clonotype_network' obsm: 'airr', 'chain_indices', 'X_clonotype_network' ir.pl.clonotype_network(mdata, color="sample", base_size=10, label_fontsize=7, panel_size=(7, 7), airr_mod='airr')画图的时候出现NaN怎样删除

1w2y3x6078 commented 3 months ago

The resulting graph looks like this. How do we remove nan, and why do we have so many nan

Thank you for your help

grst commented 3 months ago

Sorry, I can't see your example image. Likely the NAs are cells without at TCR.

grst commented 2 months ago

If you have any usage questions, please use the scverse discourse: https://discourse.scverse.org