plot,DataGeNET.Psy,ANY-method {psygenet2r} | R 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:

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

[Package psygenet2r version 1.14.0 Index]