plot_celltype_severity: Plot cell type severity

In neurogenomics/MultiEWCE: Multi-Scale Target Explorer

Plot cell type severity

Description

Plot the phenotype severity scores (generated by GPT-4) aggregated by the cell types each phenotype is significantly associated with.

Usage

plot_celltype_severity(
  results,
  cl = KGExplorer::filter_ontology(KGExplorer::get_ontology("cl"), keep_descendants =
    "cell"),
  q_threshold = 0.05,
  top_n = 3,
  types = c("bar", "dot")
)

Arguments

results	The cell type-phenotype enrichment results generated by gen_results and merged together with merge_results
cl	Cell Ontology (CL) object from KGExplorer::get_ontology("cl").
q_threshold	The q value threshold to subset the results by.
top_n	Top and bottom number of cell types to show per annotation (used in dot plot only).
types	Which types of plots of create.

Value

Named list of ggplot and data.table objects.

Examples

results <- load_example_results()
out <- plot_celltype_severity(results)

neurogenomics/MultiEWCE documentation built on Feb. 18, 2025, 6:43 p.m.