createBipartiteNet2: Plot microRNA-gene interaction network II
In YC3/mirNet: microRNA netowrk analyses

Description Usage Arguments Details Value See Also Examples

createBipartiteNet2 takes as input the output table of microRNA targets from mirDIP, and generates a microRNA-gene interaction network with two types of microRNAs and two types of targets.

createBipartiteNet2(
  miRNAs,
  filename = NULL,
  layout = layout_nicely,
  size.gene = 7,
  size.miR = 3,
  typeI_miRNA,
  typeI_target,
  typeI_miRNA_label = "Significant",
  typeII_miRNA_label = "Non-significant",
  typeI_target_label = "Up-regulated",
  typeII_target_label = "Down-regulated"
)

`miRNAs`	The output table from mirDIP.
`filename`	The desired name of the files storing `igraph` network object.
`layout`	The layout function to apply to a graph, refer to `layout_` for more details
`size.gene`	The size of the circles representing genes.
`size.miR`	The size of the squares representing microRNAs.
`typeI_miRNA`	A vector, with entries are first type of microRNAs in 'miRNA' object. The two types of microRNAs can be 'Up-regulated/Down-regulated' or 'Significantly-enriched/Nonsignificantly-enriched'.
`typeI_miRNA_label`	A short string, annotating the type I vertices of first class (microRNAs) in figure legend.
`typeII_miRNA_label`	A short string, annotating the type II vertices of first class (microRNAs) in figure legend.
`typeI_target_label`	A short string, annotating the type I vertices of second class (target mRNAs) in figure legend.
`typeII_target_label`	A short string, annotating the type II vertices of second class (target mRNAs) in figure legend.
`typeI_Target`	A vector, with entries are first type of target mRNAs in 'miRNA' object. The two types of microRNAs can be 'Up-regulated/Down-regulated'.

This function generates a bipartite network and plots the network out with two classes of vertices of different shapes. In each class of vertices there can be two subtypes, such as 'Significantly-enriched/Nonsignificantly-enriched' microRNAs and 'Up-regulated/Down-regulated' targets in microRNA network analysis.

Two rda files storing 1) the microRNA-gene interaction network object and 2) the largest connected subnetwork. A plot of the largest connected subnetwork in PDF.

igraph for all available layouts.

createBipartiteNet2(miRNAs.m, filename = 'Example_network', layout = layout_with_dh, size.gene = 4, size.miR = 4, typeI_miRNA = sig.enr.mir.v, typeI_target = mRNA.res.l$up, typeI_miRNA_label = 'Significant', typeII_miRNA_label = 'Non-significant', typeI_target_label = 'Up-regulated', typeII_target_label = 'Down-regulated')