summaryDiseases: A graphical summary of the diseases of interest.

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

Description

Given an object of class molecularComorbidity, a graphical summary of the main characteristic of the disorders is obtained.

Usage

summaryDiseases(input, database = "CURATED", type = "dis_barplot",
  assocGeneColor = "#E69F00", assocDiseaseColor = "#136593",
  dsiColor = "red", dpiColor = "black", interactive = FALSE,
  verbose = FALSE, warnings = TRUE)

Arguments

input	Object of molecularComorbidity class.
database	The default value is set to 'CURATED'. User can select any of the databases available in DisGeNET.
type	Determines if the analysis is performed for genes or diseases. By default the argument value is set to dis_barplot, allowing to analyze the number of genes associated to each one of the index diseases as well as the number of disorders that share some genes with them. It can be changed to gene_barplot to analyze and characterize the genes associated to the index diseases.
assocGeneColor	Determines the bar color that represents the number of associated genes. By default it is set to "#E69F00".
assocDiseaseColor	Determines the bar color that represents the number of associated diseases. By default it is set to "#136593".
dsiColor	Determines the dot color that represents the Disease Specificity Index (DSI). By default it is set to "red".
dpiColor	Determines the dot color that represents the Disease Pleiotropy Index (DPI). By default it is set to "black".
interactive	Determines if the output barplot 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 barplot generated with Shiny will be obtained. This argument is only available when gene_barplot type is selected.
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 barplot characterizing the genes or the disease in terms of gene-disease association.

Examples

load(system.file("extdata", "mc.RData", package="comoRbidity"))
summaryDiseases( input    = mc, 
                 type     = "dis_barplot",
                 database = "CURATED" 
           )

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