network: Plot the comorbidity analysis results in a network

In aGutierrezSacristan/comorbidity: Analyze comorbidities from electronic health record data

Description

Given an object of class cAnalysis or molecularcAnalysis obtained from a comorbidity analysis, a network is obtained.

Usage

network(input, databasePth, layout = "layout.fruchterman.reingold",
  selectValue = "score", title = "Comorbidity network", cutOff = 0,
  npairs = 0, prop = 1, interactive = FALSE, diseaseColor = "pink",
  comorColor = "lightblue", verbose = FALSE)

Arguments

input	A cAnalysis or molecularcAnalysis object, obtained by applying the comorbidityAnalysis or comorbidityAnalysisMolecular function
databasePth	Determines the path where the intermediate RData objects have been created. It is the same path where the three required input files (patientData, diagnosisData, admissionData) are located.
layout	By default 'layout.fruchterman.reingold'. It can be set to any other of the possible igraph layouts.
selectValue	By default "score" variable will be selected. Change it to any of the other possible variables ('correctedPvalue','odds ratio', 'phi', 'rr').
title	Determines the title of the network figure. By default 'Comorbidity network'.
cutOff	By default '0.05'. The value of the argument can be changed to any other numeric variable, according to the range of the selected value.
npairs	by default '0'. The value of the argument can be changed to any other numeric variable to show in the network only those comorbidities suffered by at least npairs of patients.
prop	Determines the node size proportionality. By default it is set to 1. The value of the argument can be changed to any other numeric variable.
interactive	Determines if the output network is interactive or not. By default the interactive argument is set up as FALSE. The value of the argument can be changed to TRUE, as a result an interactive network will be obtained.
diseaseColor	Determines the node color for the disorder of interest. By default it is set to "pink".
comorColor	Determines the node color for the comorbid disorders. By default it is set to "lightblue".
verbose	By default FALSE. Change it to TRUE to get a on-time log from the function.
warnings	By default TRUE. Change it to FALSE to don't see the warnings.

Value

A network

Examples

load(system.file("extdata", "comorMale.RData", package="comoRbidity"))
comorbidityNetwork <- network( 
              input            = comorMale,
              databasePth      = system.file("extdata", package="comoRbidity"), 
              selectValue      = "score",
              cutOff           = 1.5,
              npairs           = 2,
              title            = "Example comorbidity network"
              )

aGutierrezSacristan/comorbidity documentation built on April 10, 2020, 5:54 p.m.