markers_plots_top: Get a tibble of top markers extracted from each test result.

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 tibble of top markers extracted from each test result.

Description

This is basically an unnesting of filtered markers in each row of markers_processed. The filtering is based on top_n_plot and top_n_wt_plot columns in markers_plot_params.

Usage

markers_plots_top(
  markers_processed,
  markers_plot_params,
  out_dir,
  marker_type = c("global", "contrast")
)

Arguments

markers_processed	A tibble. See cluster_markers_processed or contrasts target for details.
markers_plot_params	A tibble. See cluster_markers_plot_params or contrasts_plot_params for details.
out_dir	A character scalar: path to base output directory for plots. Subdirectories and plot files will be created as ⁠<clustering_name>/<dimred>/<ENSEMBL>_<SYMBOL>_<clustering_name>_<dimred>.pdf⁠.
marker_type	A character scalar.

Value

A tibble. See cluster_markers_plots_top or contrasts_plots_top target for details.

bioinfocz/scdrake documentation built on Sept. 19, 2024, 4:43 p.m.