plotNetwork: Plot a network

In mariavica/mircomb: An R package for analyzing miRNA-mRNA interactions

Description

Plot the network of the selected miRNA-mRNa interactions, with selected features

Usage

plotNetwork(obj, pval.cutoff = 0.05, score.cutoff = NULL, sub.miRNA = NULL,
 sub.mRNA = NULL, names = TRUE, dat.sum = obj@info[["dat.sum"]],
 add.other = NULL, vertex.cex = NULL, n = NULL, node.size = 1.5)

Arguments

obj	a corObject.
pval.cutoff	p value cutoff of the selected miRNA-mRNA interactions.
score.cutoff	maximum score of the selcted miRNA-mRNA interactions.
sub.miRNA	(optional) character vector with the names of the miRNAs to be included on the plot.
sub.mRNA	(optional) character vector with the names of the mRNAs to be included on the plot.
names	Plot the names of the miRNAs and mRNAs. TRUE or FALSE.
dat.sum	minimum occurrences between databases of the selected miRNA-mRNA interactions.
add.other	Optional, character vector: name of the dataframe containing additional interactions (usually mRNA-mRNA interactions) that will also be displayed.
vertex.cex	Optional, character vector: name of the dataframe containing the relative size for each node in the network. For example "interact.table".
n	maximum number of interactions.
node.size	Size of the node

Details

The colurs are representative of the interactions. "interact.table" can be loaded from miRData package using data(interact.table).

Value

A network of the selected miRNA-mRNA interactions. Circles represent miRNAs and squares mRNAs; red fill means upregulated miRNA/mRNA, while green fill means downregulated miRNA/mRNA; lines indicate the miRNA-mRNA pairs; red line means positive score and green line means negative score; arrow width is proportional to the number of appearances on the databases.

See Also

boxplotCorrelation, plotCorrelation

Examples

data(data.obj)
data(interact.table)
plotNetwork(data.obj, pval.cutoff=0.01, dat.sum=1,
 vertex.cex="interact.table", names=FALSE)

mariavica/mircomb documentation built on Feb. 3, 2020, 2:28 a.m.