R/rfImportancePlot.R

In jasenfinch/OrbiFIEmisc: Miscellaneous functions for the analysis of FIE-HRMS data.

# Plotting function for rfImportance
#'@export

rfImportancePlot <- function(x,dn,Path,DF){		
  stats <- data.frame(x)
  stats[,ncol(stats)+1] <- seq(1,nrow(stats)) 
  stats[,ncol(stats)] <- as.factor(stats[,ncol(stats)])
  names(stats)[ncol(stats)] <- "Rank"
  suppressMessages(stats <- melt(stats))
  names(stats)[2] <- "Pairwise"
  stats[,1] <- as.numeric(as.character(stats[,1]))
  stats <- na.omit(stats)
  stats <- stats[stats$value > 0,]
  bitmap(paste(Path,DF,paste(DF,"Classification_&_Feature_Selection",sep="_"),paste(DF,dn,"RFimportance_plot.bmp",sep="_"),sep="/"))
  ggline <- ggplot(stats, aes(x=Rank, y=value, colour=Pairwise,group=Pairwise)) + 
    geom_point(size=1.5) + xlab("Rank") + ylab("Importance Score") +
    theme_bw()
  print(ggline)
  dev.off()
}