R/plot_corMatrix.R

In nicohuttmann/htmnanalysis: Analysis of Omics Data

#' Plots correlation matrix
#'
#' @param data cor.object
#' @param dendrogram should dendrogram too
#'
#' @return
#' @export
#'
#' @importFrom reshape2 melt
#' @import ggplot2
#'
#'
plot_corMatrix <- function(data, dendrogram = FALSE) {

  if(!hasArg(data)) {
    data <- getData()
  }

  if(dendrogram) {
    plot_dendrogram(data)
  }

  data.cor.melt <- data.frame(data[["cor"]][,data[["dendrogram"]]$order])

  data.cor.melt <- reshape2::melt(cbind(row.names(data.cor.melt), data.cor.melt), id.vars = 1)
  colnames(data.cor.melt) <- c("X", "Y", "value")
  data.cor.melt$X<-factor(data.cor.melt$X, levels = data.cor.melt$X[rev(data[["dendrogram"]]$order)])

  #Plot
  ggplot(data.cor.melt, aes(X, Y)) +
    geom_tile(aes(fill = value)) +
    scale_fill_gradientn(colors = c("navyblue","white","red4"), limits = c(-1, 1)) +
    theme(axis.title.x = element_blank(),
          axis.text.x = element_blank(),
          axis.ticks.x = element_blank(),
          axis.title.y = element_blank(),
          axis.ticks.y = element_blank(),
          axis.text.y = element_blank(),
          legend.position = "none")

}