plot_bar_dendro: Plot bar dendrogram

In neurogenomics/MultiEWCE: Multi-Scale Target Explorer

Plot bar dendrogram

Description

Create a plot summarising MSTExplorer results as a bar chart with multiple facets showing selected branches from the Human Phenotype Ontology (HPO). Also shows a dendrogram of celltype-celltype relationships using the Cell Ontology (CL).

Usage

plot_bar_dendro(
  results = load_example_results(),
  celltype_col = "cl_name",
  target_branches = get_target_branches(),
  keep_ancestors = names(target_branches),
  hpo = HPOExplorer::get_hpo(),
  cl = KGExplorer::get_ontology(name = "cl", lvl = 1, remove_rings = TRUE),
  facets = "ancestor_name",
  add_test_target_celltypes = TRUE,
  preferred_palettes = "tol",
  legend.position = "none",
  heights = c(0.3, 1, 0.15, 0.3),
  expand_dendro_x = rep(0.01, 2),
  q_threshold = 0.05,
  show_plot = TRUE,
  save_path = NULL,
  height = 16,
  width = 13,
  ...
)

Arguments

results	The cell type-phenotype enrichment results generated by gen_results and merged together with merge_results
celltype_col	Name of the cell type column in the results.
target_branches	A named list of HPO branches each matched with CL cell type branches that correspond to on-target cell types across the two ontologies.
keep_ancestors	Only HPO terms that have these ancestors will be kept.
hpo	Human Phenotype Ontology object, loaded from get_ontology.
cl	Cell Ontology (CL) object from KGExplorer::get_ontology("cl").
facets	A set of variables or expressions quoted by vars() and defining faceting groups on the rows or columns dimension. The variables can be named (the names are passed to labeller). For compatibility with the classic interface, can also be a formula or character vector. Use either a one sided formula, ~a + b, or a character vector, c("a", "b").
add_test_target_celltypes	Using the significant phenotype-cell type association results, run proportional enrichment tests to determine whether each cell type is overrepresented in a given HPO branch relative to all other HPO branches. Overrepresented cell types will be denoted by "*" above its bar.
preferred_palettes	Preferred palettes to use for each column.
legend.position	the default position of legends ("none", "left", "right", "bottom", "top", "inside")
heights	Passed to wrap_plots.
expand_dendro_x	Passed to scale_x_discrete in the cell type dendrogram.
q_threshold	The q value threshold to subset the results by.
show_plot	Print the plot to the console.
save_path	Save the plot to a file. Set to NULL to not save the plot.
height	Height of the saved plot.
width	Width of the saved plot.
...	Arguments passed on to EWCE::ewce_plot total_res Results data.frame generated using bootstrap_enrichment_test or ewce_expression_data functions. Multiple results tables can be merged into one results table, as long as the 'list' column is set to distinguish them. Multiple testing correction is then applied across all merged results. mtc_method Method to be used for multiple testing correction. Argument is passed to p.adjust (DEFAULT: "bonferroni). ctd CellTypeDataset object. Should be provided so that the dendrogram can be taken from it and added to plots. annotLevel An integer indicating which level of ctd to analyse (Default: 1). make_dendro Add a dendrogram (requires ctd). verbose Print messages.

Value

A bar chart with dendrogram of EWCE results in each cell type.

Examples

results <- load_example_results()
out <- plot_bar_dendro(results = results)

neurogenomics/MultiEWCE documentation built on Sept. 28, 2024, 2:27 a.m.