moduleVisual: Modules visualization and network topology

In TheJacksonLaboratory/epihet: Determining Epigenetic Heterogeneity from Bisulfite Sequencing Data

Description

Visualize the modules identified by epiNetwork() function, and calculate network topology

Usage

moduleVisual(TOM, value.matrix, moduleColors, mymodule, cutoff = 0.02,
  prefix = NULL, sve = FALSE)

Arguments

TOM	the topological overlap matrix in WGCNA generated from the epiNetwork() function
value.matrix	A data frame generated from the epiNetwork() function. the row name is patients in one subtype. the column name is the DEH loci the value in the matrix is epigenetic heterogeneity on one DEH loci for one patient
moduleColors	the module assignment generated from the epiNetwork() function
mymodule	a character vector containing the module colors you want to visulaize
cutoff	adjacency threshold for including edges in the output (default:0.02)
prefix	a character for output filename
sve	A boolean to save the plot (default: FALSE)

Value

a list containing all module edge and node information for mymodule

Examples

correlation.m<-matrix(0,12,12)
correlation.m[1,c(2:10)]<-c(0.006,0.054,0.079,0.078, 0.011,0.033,0.014,
0.023,0.034)
correlation.m[2,c(3:10)]<-c(0.026,0.014,0.045,0.037, 0.026,0.011,0.034,
0.012)
correlation.m[3,c(4:10)]<-c(0.016,0.024,0.039,0.045, 0.009,0.003,0.028)
correlation.m[4,c(5:10)]<-c(0.039,0.002,0.053,0.066, 0.012,0.039)
correlation.m[5,c(6:10)]<-c(0.019,0.016,0.047,0.046, 0.013)
correlation.m[6,c(7:10)]<-c(0.017,0.057,0.029,0.056)
correlation.m[7,c(8:10)]<-c(0.071,0.018,0.001)
correlation.m[8,c(9:10)]<-c(0.046,0.014)
correlation.m[9,10]<-0.054
correlation.m[lower.tri(correlation.m)] <-
t(correlation.m)[lower.tri(correlation.m)]

matrix.v<-matrix(0.5,5,12)
matrix.v<-as.data.frame(matrix.v)
colnames(matrix.v)<-c("NM_052960","NR_138250","NM_015074","NM_183416",
"NM_017891","NM_001330306","NM_014917","NM_001312688","NM_001330665",
"NM_017766","NM_001079843","NM_001040709")
modulecolor<-c(rep(c("yellow","cyan"),c(10,2)))
module.topology<-epihet::moduleVisual(correlation.m,
                                     value.matrix=matrix.v,
                                     moduleColors=modulecolor,
                                     mymodule="yellow",cutoff=0.02,
                                     prefix='CEBPA_sil_epipoly',sve = TRUE)

TheJacksonLaboratory/epihet documentation built on Dec. 22, 2020, 1:10 p.m.