ecotyper.rlayout¶

Write results in the R pipeline’s directory layout and file formats (write.table(x, sep = "\t")), so outputs can be diffed with R’s.

Functions

`write_ecotype_recovery`(res, out_dir)	Files of `Ecotypes/recovery/<dataset>/`.
`write_recovery_output`(state_results, eco, ...)	The user-facing `RecoveryOutput/<dataset>/` folder (subset of files copied by the R wrappers).
`write_state_recovery`(res, out_dir)	Files of `Cell_States/recovery/<dataset>/<cell type>/<rank>/`.

ecotyper.rlayout.write_state_recovery(res, out_dir)[source]¶

Files of Cell_States/recovery/<dataset>/<cell type>/<rank>/.

Parameters:: res (StateRecovery)
Return type:: None

ecotyper.rlayout.write_ecotype_recovery(res, out_dir)[source]¶

Files of Ecotypes/recovery/<dataset>/.

Parameters:: res (EcotypeRecovery)
Return type:: None

ecotyper.rlayout.write_recovery_output(state_results, eco, out_dir, cell_types, state_files=('state_abundances.txt', 'state_assignment.txt', 'heatmap_data.txt', 'heatmap_top_ann.txt'))[source]¶

The user-facing RecoveryOutput/<dataset>/ folder (subset of files copied by the R wrappers).

Parameters:

state_results (dict)
eco (EcotypeRecovery | None)

Return type:

None