sccloud.tools.run_scp_output

sccloud.tools.run_scp_output(input_h5ad_file, output_name, is_sparse=True, round_to=2)[source]

Generate outputs for single cell portal.

Parameters

  • input_h5ad_file (str) – Input h5ad file name.

  • output_name (str) – Name prefix for output files.

  • is_sparse (bool, optional, default: True) – If True, enforce the count matrix to be sparse after written into files.

  • round_to (int, optional, default: 2) – Round numbers to round_to decimal places.

Returns

  • None

  • Generate several files –

    • output_name.scp.basis.coords.txt, where basis is for each key in adata.obsm field.

    • output_name.scp.metadata.txt.

    • Gene expression files:
      • If in sparse format:

        • output_name.scp.features.tsv, information on genes;

        • output_name.scp.barcodes.tsv, information on cell barcodes;

        • output_name.scp.matrix.mtx, count matrix.

      • If not in sparse:

        • output_name.scp.expr.txt.

Examples

>>> scc.run_scp_output("result.h5ad", output_name = "scp_result")