moduleVisual: Modules visualization and network topology

Description Usage Arguments Value Examples

View source: R/moduleVisual.R

Description

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

Usage

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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

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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.