markers_for_tables: Make a table used in HTML report of marker results.

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

Make a table used in HTML report of marker results.

Description

It combines marker statistics, parameters, dimred plots, and links to heatmaps.

Usage

markers_for_tables(
  markers_out,
  markers_heatmaps_df,
  markers_plots_top,
  markers_dimred_plots_files,
  out_dir,
  ensembl_species = "Homo_sapiens",
  ...
)

Arguments

markers_out	A tibble. See cluster_markers_out or contrasts_out target for details.
markers_heatmaps_df	A tibble. See cluster_markers_heatmaps_df or contrasts_heatmaps_df for details.
markers_plots_top	A tibble. See cluster_markers_plots_top or contrasts_plots_top for details.
markers_dimred_plots_files	A tibble. See cluster_markers_dimred_plots_files or contrasts_dimred_plots_files for details.
out_dir	A character scalar: path to base output directory to save HTML tables in. Files and subdirectories will be created as: ⁠<source_name>/<source_name>_<test_type>_<group_level>.html⁠ for cluster markers. Example: markers_cluster_kmeans_k4/markers_cluster_kmeans_k4_t_1.html ⁠<source_name>/<source_name>_<test_type>_<target_level>_vs_<reference_level>.html⁠ for contrasts. Example: dea_cluster_louvain_annotated/dea_cluster_louvain_annotated_binom_cl3_vs_cl4.html
ensembl_species	A character scalar: passed to add_marker_table_links().
...	Currently not used.

Value

A tibble. See cluster_markers_for_tables or contrasts_for_tables for details.

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