Main functions — main • HPOExplorer

Main functions.

annotate_phenos(
  phenos,
  hpo = get_hpo(),
  add_ont_lvl_absolute = TRUE,
  add_ont_lvl_relative = FALSE,
  add_info_content = TRUE,
  add_description = TRUE,
  add_disease_data = FALSE,
  add_ndiseases = add_disease_data,
  add_onsets = add_disease_data,
  add_deaths = add_disease_data,
  add_pheno_frequencies = add_disease_data,
  add_tiers = add_disease_data,
  add_severities = add_disease_data,
  add_disease_definitions = add_disease_data,
  include_mondo = FALSE,
  add_hoverboxes = FALSE,
  columns = list_columns(),
  interactive = TRUE
)

example_phenos(i = seq(10), hpo = get_hpo())

Arguments

phenos: A data.table containing HPO IDs and other metadata.
hpo: Human Phenotype Ontology object, loaded from get_ontology.
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.
add_info_content: Add information content column for each phenotype.
add_description: Whether to get the phenotype descriptions as well (slower).
add_disease_data: Add all disease metadata columns. This will expand the data using allow.cartesian=TRUE.
add_ndiseases: Add the number of diseases per phenotype.
add_onsets: Add age of onset columns using add_onset.
add_deaths: Add age of death columns using add_death.
add_pheno_frequencies: Add the frequency of each phenotype in each disease.
add_tiers: Add severity Tiers column using add_tier.
add_severities: Add severity column using add_severity.
add_disease_definitions: Add disease definitions.
include_mondo: Add MONDO IDs, names, and definitions to each disease.
add_hoverboxes: Add hoverdata with add_hoverboxes.
columns: A named vector of columns in phenos to add to the hoverdata via add_hoverboxes.
interactive: Make the plot interactive.
i: Indices of HPO IDs to use.

Value

Data.

phenotype data.table

Functions

annotate_phenos(): main Annotate phenotypes

Annotate phenotypes data.table without various types of metadata.
example_phenos(): main Example phenotypes dataframe

Create a minimal example of a phenos dataframe.

Examples

phenos <- example_phenos()
phenos2 <- annotate_phenos(phenos)
#> Adding HPO names.
#> Translating ontology terms to names.
#> Adding term definitions.
#> Adding level-2 ancestor to each HPO ID.
#> Adding ancestor metadata.
#> Ancestor metadata already present. Use force_new=TRUE to overwrite.
#> 10 associations remain after filtering.
#> Getting absolute ontology level for 19,025 IDs.
#> Adding information_content scores.
phenos <- example_phenos()