get_cell_annotation_subplan: Get a subplan for cell annotation via 'SingleR'

In bioinfocz/scdrake: A pipeline for droplet-based single-cell RNA-seq data secondary analysis implemented in the drake Make-like toolkit for R language

Get a subplan for cell annotation via SingleR

Description

Get a subplan for cell annotation via SingleR

Usage

get_cell_annotation_subplan(
  sce_target_name,
  sce_dimred_plots_target_name,
  cell_annotation_sources,
  cell_annotation_out_dir,
  report_dimred_names,
  dimred_plots_out_dir,
  do_heatmaps_
)

Arguments

sce_target_name, sce_dimred_plots_target_name	A character scalar: name of target representing a SCE object that will be used for cell annotation or dimred plots.
cell_annotation_sources	A tibble with cell annotation parameters.
cell_annotation_out_dir	A character scalar: output directory for diagnostic plots.
report_dimred_names	A character vector: dimred names for plots.
dimred_plots_out_dir	A character scalar: output directory for dimred plots.
do_heatmaps_	A logical scalar: if TRUE, make heatmaps annotated by predicted cell types and cluster memberships.

Value

drake::drake_plan()

bioinfocz/scdrake documentation built on Jan. 29, 2024, 10:24 a.m.