R/simplePCA.R

In nicohuttmann/htmnanalysis: Analysis of Omics Data

#' Simple PCA plot
#'
#' @return
#' @export
#'
#' @importFrom ggplot2 autoplot
#' @import ggfortify
#'
#'
simplePCA <- function() {

  message("")
  message("Define data.")
  data <- getDataFrame()

  message("")
  message("Define group.")
  group <- getVector()

  group <- group[intersect(names(group), rownames(data))]

  data <- data[names(group), ]



  message("")
  message("Column names: ")
  print(head(colnames(data)))

  if(readline("Specify subgroup to process? (ja/nein) ") == "ja") {

    data <- data[, setSubGroup(colnames(data))]

  }

  group <- group[rownames(data)]




  message("Ready to process.")

  data <- scale(data) #Add protein groups


  data.pca <- prcomp(data)


  message("Principal components computed.")

  done <- "nein"

  while(done != "ja") {

    pcx <- as.numeric(readline("Principal component x: "))
    pcy <- as.numeric(readline("Principal component y: "))

    if(pcx %in% 1:nrow(data) && pcy %in% 1:nrow(data)) {
      print(autoplot(data.pca, data = cbind(Set = group, data), colour = "Set", x = pcx, y = pcy))
    }

    done <- readline("Done? ")

  }


}