geneAttrPlot-methods: Ploting the relation between genes and disease-categories

In aGutierrezSacristan/psygenet2r: psygenet2r - An R package for querying PsyGeNET and to perform comorbidity studies in psychiatric disorders

Ploting the relation between genes and disease-categories

Description

Given a set of genes or a result of psygenetGene creates four types of plots showing the relation of the genes with the disease's category in psyGeNET.

Usage

geneAttrPlot(x, type = "pie", ..., verbose = FALSE)

Arguments

x	Vector of genes of interest of DataGeNET.Psy resulting of psyegnetDisease.
type	Type of the drawn chart. By default it is "pie". It can takes "pie" to plot a pie chart with the number of genes for each psychiatric category, "disease category" for visualizing a barplot with the total and specific number of genes for each psychiatric disorder, "evidence index" for a barplot showing for each psychiatric disorder the number of gene-disease associations according to the Evidence index and "gene" for visualizing a barplot with the total and specific number of diseases associated to each gene.
...	(Check NOTE section) Passed to inner functions for different plots.
verbose	By default FALSE. Change it to TRUE to get a on-time log from the function.

Value

A plot for a DataGeNET.Psy in terms of the panther-class.

Note

The "Evidence Index" is gotten from PsyGeNET. For more information about it and its calculation, pease visit psygenet.org. Argument ... can be filled with specific argument depending on the type of plot:

Type	Argument	Color	Description
gene	cuiBarColor	Purple	Determines the color of the bar for diseases
	diseaseCategoryBarColor	Yellow	Determines the color of the bar for psychiatric categories
disease category	uniqueGenesBarColor	Orange	Determines the color of the bar for unique genes for a disease category
	totalGenesBarColor	Blue	Determines the color of the bar for total genes for a disease category

aGutierrezSacristan/psygenet2r documentation built on Jan. 18, 2024, 4:06 a.m.