plot_bar_summary: Summary plot

In neurogenomics/MultiEWCE: Multi-Scale Target Explorer

Summary plot

Description

Generate a plot summarising the cell type-phenotype enrichment results generated by gen_results.

Usage

plot_bar_summary(
  results = load_example_results(),
  count_var = "hpo_name",
  group_var = "CellType",
  keywords = NULL,
  q_threshold = 5e-04,
  effect_threshold = 1,
  filters = NULL,
  keep_descendants = NULL,
  hpo = HPOExplorer::get_hpo(),
  option = "magma",
  interactive = TRUE,
  show_plot = TRUE,
  verbose = TRUE
)

Arguments

results	The cell type-phenotype enrichment results generated by gen_results and merged together with merge_results
count_var	Variable to get counts for per group_var.
group_var	Variable to group counts by.
keywords	Keywords supplied to search for phenotypes. Will be used to generate the plot title.
q_threshold	The q value threshold to subset the results by.
effect_threshold	The minimum fold change in specific expression to subset the results by.
filters	A named list, where each element in the list is the name of a column in the data, and the vector within each element represents the values to include in the final data.
keep_descendants	Terms whose descendants should be kept (including themselves). Set to NULL (default) to skip this filtering step.
hpo	Human Phenotype Ontology object, loaded from get_ontology.
option	A character string indicating the color map option to use. Eight options are available: "magma" (or "A") "inferno" (or "B") "plasma" (or "C") "viridis" (or "D") "cividis" (or "E") "rocket" (or "F") "mako" (or "G") "turbo" (or "H")
interactive	Make the plot interactive.
show_plot	Show the plot.
verbose	Print messages.

Value

ggplot or plotly object

Examples

keep_descendants <- "Neurodevelopmental delay"
plt_pheno_count <- plot_bar_summary(count_var = "hpo_name",
                                group_var = "CellType",
                                keep_descendants = keep_descendants)
plt_cell_count <- plot_bar_summary(count_var = "CellType",
                                group_var = "hpo_name",
                                keep_descendants = keep_descendants)

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