stereo.algorithm.spa_track.SpaTrack.order_trajectory_genes

SpaTrack.order_trajectory_genes(gam_result, min_model_fit=0, max_fdr=1, cell_number=20)[source]

Split cells sorted by ptime into widonws.

Order genes according number id of the maximum expression window.

Only running on the subset of cells that are the neighbors of the LAP.

Parameters:

  • gam_result (DataFrame) – the result of spt.ptime_gene_GAM.

  • min_model_fit (float) – the minimum model fit for filtering the gam result, defaults to 0

  • max_fdr (float) – the maximum fdr for filtering the gam result, defaults to 1

  • cell_number (int) – Cell number within splited window, defaults to 20

Returns:

A DataFrame whose columns are sortted significant genes expression matrix according to mean expression value in windows and index is cells.