plot-DataGeNET.Psy-ANY-method: Plots the content of a 'DataGeNET.Psy' object

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

Plots the content of a DataGeNET.Psy object

Description

This functions llows to create a variety of plots for DataGeNEt.Psy and JaccardIndexPsy objects.

Usage

## S4 method for signature 'DataGeNET.Psy,ANY'
plot(x, y,
  layout = igraph::layout.fruchterman.reingold, type = "GDA network",
  verbose = FALSE, ...)

Arguments

x	Object of class DataGeNET.Psy
y	NOT USED
layout	Function to design the location of the different nodes. By default layout.fruchterman.reingold from igraph is used.
type	Type of the drawn chart. By default it is "GDA network" but it also can be "GDCA network", "GDCA heatmap", "GDA heatmap" and "publications". The first two are network representations of the second two. While the last one draws a barplot with the number of PMIDs between genes and diseases.
verbose	By default FALSE. If set to TRUE information on the drawing process will be shown.
...	(Check NOTE section) Passed to inner functions for different plots.

Value

A plot for DataGeNET.Psy.

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
GDA network	geneColor	Yellow	Determines the color of the gene nodes
	diseaseColor	Blue	Determines the color of the disease nodes
GDA heatmap	highColor	Blue	Determines the color of the heatmap for the highest value
	lowColor	White	Determines the color of the heatmap for the lowest value
GDCA network	ei0color	Yellow	Determines the color for those associations with evidence index 0
	eiAmbiguitcolor	Grey	Determines the color for those associations with evidence index greater than 0 and lower than 1
	ei1color	Blue	Determines the color for those associations with evidence index 1
GDCA heatmap	AUDcolor	#FF3C32
	BDcolor	#FFC698
	DEPcolor	#9BE75E
	SCHZcolor	#1F6024
	CUDcolor	#5AB69C
	SIDEPcolor	#50B8D6
	CanUDcolor	#5467C3
	SYPSYcolor	#A654C3
	geneColor	Orange

Examples

data(qr)
plot(qr) # for all-disease plot
plot(qr, type = 'GDCA network') # for MPI plot

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