Description Usage Arguments Details Value Author(s) Examples
Graphical Representation of TF2target_DCL-centered and TF_bridged_DCL-centered networks
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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. |
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).
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. |
Jing Yang, Hui Yu
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 | 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,]
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