labeling_info

besca.export.labeling_info(outpath: Optional[str] = None, description: str = 'leiden clustering', public: bool = False, default: bool = True, expert: bool = False, reference: bool = False, method: str = 'leiden', annotated_version_of: str = '-', filename: str = 'labelinfo.tsv') → None[source]

write out labeling info for uploading to database

This functions outputs the file labelinfo.tsv which is needed to annotate a written out labeling in the scseq database.

Parameters:

  • outpath (str | default = current working directory) – The filepath as a string indicating the location where the file should be written out to.

  • description (str | default = ‘leiden clustering’) – string describing what type of information is saved in the corresponding labeling.

  • public (bool | default = False) – boolian indicator if the contained labeling information is available in the public domain.

  • True (default bool | default =) – boolian indicator if the labeling was created using a standardized process e.g. the leiden clusters outputed by the standard pipeline (this should be false if expert is true)

  • expert (bool | default = False) – boolian indicator if the labeling was created by an ‘expert’ i.e. manually done (this should be false if default is true)

  • reference (bool | default = True) – boolian indicator if this is the labeling (e.g. celltype annotation) that should be used for further analysis (there should only be one reference labeling per study)

  • method (str | default = ‘leiden’) – string indicating the type of method that was applied, e.g. if the labeling is of a clustering which clustering algorithm was used.

  • annotated_version_of (str | default = ‘-’) – string identifying of what othe labeling/dataset this is an annotated version of (so for example if the labeling is celltype annotation of a leiden clustering then this would reference the leiden clsutering that was used to obtain the clusters that were then labeled here)

  • filename (str | default = ‘labelinfo.tsv’) – string indicating the filename that should be used. This is per default set to the correct file name for uploading to the scseq database.

Returns:

results are written out to a file instead

Return type:

None