Make a table used in HTML report of marker results. — markers_for

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.