generate_cell_annotation_plots_section: Generate a section with dimred plots used in some RMarkdown...

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

Generate a section with dimred plots used in some RMarkdown files.

Description

The hierarchy is composed of tabsets:

• Selected annotation reference

  • Dimred plots (UMAP, t-SNE, PCA)

Usage

generate_cell_annotation_plots_section(
  dimred_plots_cell_annotation_files,
  cell_annotation_diagnostic_plots,
  dimred_plots_rel_start = ".",
  cell_annotation_diagnostic_plots_rel_start = ".",
  main_header = "Cell annotation",
  main_header_level = 1,
  text = NULL
)

Arguments

dimred_plots_cell_annotation_files	A tibble.
cell_annotation_diagnostic_plots	A tibble or NULL.
dimred_plots_rel_start, cell_annotation_diagnostic_plots_rel_start	A character scalar: relative start of path to directory with dimred plots, selected markers or cell annotation diagnostic plots PDFs. See the Relative links section in create_a_link().
main_header	A character scalar: text of the main header.
main_header_level	A numeric scalar: level of the main header.
text	A character text: additional text to be displayed on top of the section.

Value

Invisibly NULL.

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