Visualisation {IntramiRExploreR} | R Documentation |
Visualises the targetGene:miRNA network using Cytoscape and igraph .
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"))
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'. |
Depending upon the ouput choice network image or dataframe containg miRNAs that target the query gene are ouput.
miRNA='dme-miR-12' Visualisation(miRNA,mRNA_type=c('GeneSymbol'),method=c('Pearson'), platform=c('Affy1'),visualisation=c('igraph'),layout=c('kamadakawai'), path=tempdir())