Visualisation {IntramiRExploreR}

R Documentation

Visualises the targetGene:miRNA network using Cytoscape and igraph .

Description

Visualises the targetGene:miRNA network using Cytoscape and igraph .

Usage

Visualisation(
  miRNA,
  mRNA_type = c("GeneSymbol", "FBID", "CGID"),
  method = c("Pearson", "Distance", "Both"),
  platform = c("Affy1", "Affy2"),
  thresh = 50,
  visualisation = c("igraph", "Cytoscape", "Text", "console"),
  path = tempdir(),
  layout = c("kamadakawai", "reingold.tilford", "fruchterman.reingold", "interactive")
)

Arguments

miRNA	character. miRNA Identifier.
mRNA_type	character. mRNA id type. The choices are 'GeneSymbol','FBID' and 'CGID'.
method	character. Statistical Methods. Choices are 'Pearson','Distance','Both'
platform	character. Affymetrix Platforms. Choices are 'Affy1','Affy2'.
thresh	integar. Threshold depicting number of rows to show.
visualisation	character.Visualisation type. Choices are 'igraph','Cytoscape','text' and 'console'.
path	character. Path where data.frame is saved when visualisation is text. Default is tempdir().
layout	character. Network choices. Choices are 'kamadakawai','reingold.tilford','fruchterman.reingold' and 'interactive'.

Value

Depending upon the ouput choice network image or dataframe containg miRNAs that target the query gene are ouput.

Examples

miRNA='dme-miR-12'
Visualisation(miRNA,mRNA_type=c('GeneSymbol'),method=c('Pearson'),
platform=c('Affy1'),visualisation=c('igraph'),layout=c('kamadakawai'),
           path=tempdir())

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