ggnetwork_plot_full: Create interactive network plot start to finish

In neurogenomics/MultiEWCE: Multi-Scale Target Explorer

Create interactive network plot start to finish

Description

This puts all the functions together from getting the subset of results to creating the final interactive plot.

Usage

ggnetwork_plot_full(
  filters,
  keep_descendants = NULL,
  results = load_example_results(),
  hpo = HPOExplorer::get_hpo(),
  q_threshold = 5e-04,
  effect_threshold = 1,
  columns = HPOExplorer::list_columns(),
  colour_var = "effect",
  size_var = "ontLvl_relative",
  add_ont_lvl_absolute = TRUE,
  add_ont_lvl_relative = TRUE,
  method = c("ggnetwork", "visnetwork"),
  interactive = TRUE,
  verbose = TRUE,
  ...
)

Arguments

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.
results	The cell type-phenotype enrichment results generated by gen_results and merged together with merge_results
hpo	Human Phenotype Ontology object, loaded from get_ontology.
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.
columns	A named vector of columns in phenos to add to the hoverdata via add_hoverboxes.
colour_var	The column from phenos that you wish to map to node colour.
size_var	Column to scale node size by.
add_ont_lvl_absolute	Add the absolute ontology level of each HPO term. See get_ontology_levels for more details.
add_ont_lvl_relative	Add the relative ontology level of each HPO term. See get_ontology_levels for more details.
method	Method to construct plot with.
interactive	Make the plot interactive.
verbose	Print messages.
...	Arguments passed on to HPOExplorer::make_network_plot phenos A data.table containing HPO IDs and other metadata. label_var Column containing the label for each node in a graph (e.g. "hpo_name"). show_plot Show the plot. hoverbox_column Name of the new hoverbox column to add. preferred_palettes Preferred palettes to use for each column.

Value

A named list of outputs, including a interactive network plot of the selected subset of results from RD EWCE analysis.

Examples

res <- ggnetwork_plot_full(filters = list(CellType = "Microglia"))

neurogenomics/MultiEWCE documentation built on April 22, 2024, 6:22 a.m.