scSemiProfiler.singlecell_process.scprocess

scSemiProfiler.singlecell_process.scprocess(name, singlecell, logged=False, normed=True, cellfilter=False, threshold=0.001, geneset=True, weight=0.5, k=15)[source]

Process the reprsentatives’ single-cell data, including preprocessing and feature augmentations.

Parameters

  • name (str) – Project name.

  • singlecell (str) – Path to representatives’ single-cell data.

  • logged (bool) – Whether the data has been logged or not

  • normed (bool) – Whether the library size has been normalized or not

  • cellfilter (bool) – Whether to perform standard cell filtering.

  • threshold (float) – Threshold for background noise removal.

  • geneset (typing.Union[bool, str]) – Whether to use gene set to augment gene expression features or no.

  • weight (float) – The proportion of top features to increase importance weight.

  • k (int) – K for the K-NN graph built for cells.

Return type

None

Returns

None

Example

>>> scSemiProfiler.scprocess(name = 'project_name', singlecell = name+'/representative_sc.h5ad', logged = False, normed = True, cellfilter = False, threshold=1e-3, geneset=True, weight = 0.5, k = 15)