make_: Make functions

In neurogenomics/HPOExplorer: Analysis and Visualisation of the Human Phenotype Ontology

Make functions

Description

Functions to make complex R objects.

Usage

make_igraph_object(
  phenos,
  hpo = get_hpo(),
  colour_var = "fold_change",
  cols = list_columns(extra_cols = c(colour_var, grep("_count$|_values$", names(phenos),
    value = TRUE))),
  ...
)

make_network_object(
  phenos,
  hpo = get_hpo(),
  colour_var = "fold_change",
  add_ont_lvl_absolute = FALSE,
  cols = list_columns(extra_cols = c(colour_var, grep("_count$|_values$", names(phenos),
    value = TRUE))),
  as = c("ggnetwork", "tbl_graph"),
  ...
)

make_network_plot(
  phenos,
  colour_var = "ontLvl",
  size_var = colour_var,
  label_var = "hpo_name",
  interactive = TRUE,
  show_plot = TRUE,
  hoverbox_column = "hover",
  preferred_palettes = "brewer.reds",
  method = c("ggnetwork", "visnetwork"),
  ...
)

make_phenos_dataframe(
  ancestor = NULL,
  hpo = get_hpo(),
  phenotype_to_genes = load_phenotype_to_genes(),
  add_ont_lvl_absolute = TRUE,
  add_ont_lvl_relative = FALSE,
  add_info_content = FALSE,
  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,
  verbose = TRUE
)

make_tiers(
  hpo = get_hpo(),
  terms = hpo@terms,
  keyword_sets = list(Tier1 = c("intellectual disability", "death"), Tier2 =
    c("impaired mobility", "malform"), Tier3 = c("sight", "vision", "immunodeficien",
    "cancer", "hearing", "touch", "pain ", " pain", "mental illness", "dysmorphic"),
    Tier4 = c("fertility")),
  check_names = TRUE,
  check_definitions = TRUE,
  check_diseases = FALSE,
  search_ancestors = TRUE,
  search_descendants = TRUE,
  as_datatable = FALSE,
  verbose = TRUE
)

Arguments

phenos	A data.table containing HPO IDs and other metadata.
hpo	Human Phenotype Ontology object, loaded from get_ontology.
colour_var	The column from phenos that you wish to map to node colour.
cols	Columns to add to metadata of ggnetwork object.
...	Arguments passed on to make_network_object
add_ont_lvl_absolute	Add the absolute ontology level of each HPO term. See get_ontology_levels for more details.
as	R object class to return output as.
size_var	Column to scale node size by.
label_var	Column containing the label for each node in a graph (e.g. "hpo_name").
interactive	Make the plot interactive.
show_plot	Show the plot.
hoverbox_column	Name of the new hoverbox column to add.
preferred_palettes	Preferred palettes to use for each column.
method	Method to construct plot with.
ancestor	The ancestor to get all descendants of. If NULL, returns the entirely ontology.
phenotype_to_genes	Output of load_phenotype_to_genes mapping phenotypes to gene annotations.
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.
verbose	Print messages.
terms	A subset of HPO IDs to assign Tiers to.
keyword_sets	A named list of regex queries to be used when searching for phenotypes that have matching metadata.
check_names	When regexsearching for matching terms, check the phenotype names.
check_definitions	When regex searching for matching terms, check the phenotype definition.
check_diseases	When regex searching for matching terms, check the names of diseases associated with the phenotype.
search_ancestors	Inherit Tiers of ancestors.
search_descendants	Inherit Tiers of descendants.
as_datatable	Return the results as a data.table.

Value

R object.

A igraph object.

A ggnetwork object.

A named list containing the graph data and the plot.

The HPO in dataframe format.

Tier assignments for each term in terms. Will be returned as either a named vector or a data.table.

Functions

• make_igraph_object(): make_ Make an igraph object

  This uses the network package to coerce the adjacency matrix into a network object. It also adds the fold change, label, and relative ontology level parameters to each node in the network.

  It expects there to be a column of HPO IDs in the phenos dataframe called hpo_id.

• make_network_object(): make_ Make a ggnetwork object

  This uses the network package to coerce the adjacency matrix into a network object. It also adds the fold change, label, and relative ontology level parameters to each node in the network.

  It expects there to be a column of HPO IDs in the phenos dataframe called hpo_id.

• make_network_plot(): make_ Generate network plot

  This creates a network plot. It makes it possible to hover box that includes your results related to each phenotype and/or a description of the phenotypes.

• make_phenos_dataframe(): make_ Make phenotypes dataframe

  Make a dataframe from a subset of the Human Phenotype Ontology.

• make_tiers(): make_ Make severity Tiers (auto)

  Automatically add severity Tier for each HPO ID, in accordance with the rating system provided by Lazarin et al (2014). In order of increasing severity:

  • Tier 4 Reduced fertility

  • Tier 3 Sensory impairment: vision, Immunodeficiency/cancer, Sensory impairment: hearing, Sensory impairment: touch, other (including pain), Mental illness, Dysmorphic features

  • Tier 2 Shortened life span: premature adulthood, Impaired mobility, Internal physical malformation

  • Tier 1 Shortened life span: infancy, Shortened life span: childhood/adolescence, Intellectual disability

Examples

phenos <- make_phenos_dataframe(ancestor = "Neurodevelopmental delay")
g <- make_igraph_object(phenos = phenos)
phenos <- make_phenos_dataframe(ancestor = "Neurodevelopmental delay")
phenoNet <- make_network_object(phenos = phenos,
                                colour_var = "ontLvl_geneCount_ratio")
phenos <- make_phenos_dataframe(ancestor = "Neurodevelopmental delay")
plt <- make_network_plot(phenos = phenos)
phenos <- make_phenos_dataframe(ancestor = "Neurodevelopmental delay")
terms <- get_hpo()@terms[seq(100)]
tiers <- make_tiers(terms = terms)

neurogenomics/HPOExplorer documentation built on Aug. 24, 2024, 1:39 a.m.