setup_network_data: Convert phenotype dataframe to a data list that works with...

In tbilab/meToolkit: Build and Customize Phewas Multimorbidity Explorer Apps.

Description

Helper functions related to the networks module Takes a subset of the individual data along with phewas results and returns a set of network data in the form of edges and vertices as required by network_plot.

Usage

setup_network_data(
  data,
  phecode_info,
  inverted_codes = c(),
  case_size = 0.1,
  code_size = 0.3,
  no_copies = "#bdbdbd",
  one_copy = "orangered",
  two_copies = "red"
)

Arguments

data	A phenome dataframe with phecodes as columns and also with an IID column and a snp status column
phecode_info	Information about each codes results in phewas study in form of columns: code, category, color, tooltip.
inverted_codes	An array of codes that are inverted. Note that if a code is inverted that should also be reflected in data. This is only for visual modifications.
case_size	Size of nodes drawn for cases (default of 0.1)
code_size	Size of nodes drawn for phecodes (default of 0.3)
no_copies	Color of cases nodes with no minor allele copy (default grey)
one_copy	Color of cases nodes with one minor allele copy (default orangered)
two_copies	Color of cases nodes with two minor allele copies (default redish)

Value

A list containing two dataframes: vertices a dataframe containing each unique node in network (all unique IIDs and Phecodes) along with columns snp_status, name, color, size, selectable, id, tooltip which are all attributes used by the various network plotting functions included in library edges: a dataframe with columns source and target corresponding to the edges between each vertices according to the assigned interger id.

Examples

setup_network_data(data, phewas_results)

tbilab/meToolkit documentation built on June 23, 2020, 9:55 a.m.