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

plot,DataGeNET.Psy,ANY-methodR Documentation

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:

TypeArgument 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.