DRplot: Visualization of DRLs

In DCGL: Differential Co-expression Analysis and Differential Regulation Analysis of Gene Expression Microarray Data

Description

Graphical Representation of TF2target_DCL-centered and TF_bridged_DCL-centered networks

Usage

DRplot(DCGs, DCLs, tf2target, expGenes,
	type = c("both", "TF2target_DCL", "TF_bridged_DCL")[1], 
	intgenelist = NULL, 
	vsize=5,asize=0.25,lcex=0.3,ewidth=1,
	figname = c("TF2target_DCL.pdf", "TF_bridged_DCL.pdf"))

Arguments

DCGs	a data frame or matrix for DCGs list.
DCLs	a data frame or matrix for DCLs list.
tf2target	a data frame or matrix for TF-to-target interaction pairs.
expGenes	a list for measured genes by array
type	a character string to determine which type of DRLs ('TF2target_DCL' or 'TF_bridged_DCL' or 'both') will be plotted; default is 'both'.
intgenelist	a list of gene symbols, which contains only one column to display your interesting genes symbol; default is NULL
vsize	a numeric of node size
asize	a numeric of arrow size
lcex	a numeric of lable size
ewidth	a numeric of edge width
figname	two character strings of graph names.

Details

We built a function DRplot to display combined information of DCGs/DCLs and DRGs/DRLs. DRpolt generates two figures which are 1): TF2target_DCL-centered network and 2): TF_bridged_DCL-centered network. In both networks, we rely on different node shapes differentiate TFs and non-TFs (square for TFs, circle for non-TFs), different node colors to categorize genes (pink for DCGs, blue for non-DCGs, gray for TFs which are not tested in expression microarray data), and different edge types to express different relations of gene pairs (solid for DCLs, dashed for non-DCLs; edges with arrow indicate TF-to-target relations).

Value

One or Two graphs as users' wish have been saved in currently working directory. And a list of two components:

TF2target_DCL	One kind of DRLs termed TF2target_DCL.
TF_bridged_DCL	Another kind of DRLs termed TF_bridged_DCL.

Author(s)

Jing Yang, Hui Yu

Examples

data(exprs)
## divide exprs into two parts corresponding to condition 1 
## (exprs.1) and condition 2 (exprs.2) respectively
exprs.1<-exprs[1:100,1:16]
exprs.2<-exprs[1:100,17:63]
expGenes<-rownames(exprs)

data(tf2target)
DCp.res<-DCp(exprs.1,exprs.2,link.method = 'qth',cutoff=0.25)
DCe.res<-DCe(exprs.1,exprs.2,link.method = 'qth',cutoff=0.25,nbins=10,p=0.1)
DCsum.res<-DCsum(DCp.res,DCe.res,DCpcutoff=0.25,DCecutoff=0.4)
DRplot.res<-DRplot(DCsum.res$DCGs,DCsum.res$DCLs,
	tf2target,
	expGenes,
	type='TF_bridged_DCL',
	intgenelist=NULL,
	vsize=5,asize=0.25,lcex=0.3,ewidth=1,
	figname=c('TF2target_DCL.pdf','TF_bridged_DCL.pdf'))

## two types of Differentially Regulated Links which were plotted
DRplot.res$TF2target_DCL[1:3,]
DRplot.res$TF_bridged_DCL[1:3,]

## plot sub-network by predefined gene(s)
data(intgenelist)
DRplot.int.res<-DRplot(DCsum.res$DCGs,DCsum.res$DCLs,
	tf2target,
	expGenes,
	type='TF_bridged_DCL',
	intgenelist=intgenelist,
	vsize=5,asize=0.25,lcex=0.3,ewidth=1,
	figname=c('TF2target_DCL_int.pdf','TF_bridged_DCL_int.pdf'))
DRplot.int.res$TF2target_DCL[1:3,]
DRplot.int.res$TF_bridged_DCL[1:3,]

DCGL documentation built on May 1, 2019, 8:38 p.m.