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

Description Usage Arguments Value Note

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

1
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

psygenet2r documentation built on Jan. 31, 2021, 2 a.m.