genericqgraph: qgraph plot

In ShouyeLiu/metaboliteUtility:

Description

qgraph plot

Usage

genericqgraph(tmpCor, titleName = "", labels = colnames(tmpCor),
  esize = 20, alpha = 0.05, cut = NULL, maximum = 1,
  palette = "pastel", posCol = "red", negCol = "blue", details = TRUE,
  layout = "spring", label.cex = 0.9, label.prop = 0.9,
  label.fill.horizontal = 1, shape = "ellipse", ...)

Arguments

tmpCor

correlation matrix

Details

Please see qgraph

Examples

 data(corrplot_data)
 metaname <-names(corrplot_data)
 tmpDataset <- as.matrix(corrplot_data);

 set.seed(1)
 Pathway <- sort(paste0("p",as.integer(runif(length(metaname), 0, 1)*3+1)))
 step 3, handle pathway info
 pathwayData <- data.frame(Var= (metaname),
                           Pathway = ((Pathway)))
 # generate suitable group index
 qgraph_path <- pathwayData[with(pathwayData, order(Pathway)), ] # sort data frame by column Pathway
 qgraph_path$Var <- as.character(qgraph_path$Var)
 tmp <- tmpDataset[,c(qgraph_path$Var)] # select pathway subset according to sorted order
 qgraph_groups <- as.character(qgraph_path$Pathway); # generate group index
 sample_size <- nrow(tmp)
 tmpCor <- cor(tmp, use ="pairwise.complete.obs" ,method="pearson");
 genericqgraph(tmpCor,groups=qgraph_groups,graph = "pcor",
               sampleSize=sample_size,title=paste(sub_time,gen,"partial corre"),
               threshold = "BH",minimum  = "sig",
 );

ShouyeLiu/metaboliteUtility documentation built on May 6, 2019, 9:07 a.m.