R/Graphics.R

In tommasorigon/PhDPack: Useful script to survive PhD

multiplot <- function(..., plotlist=NULL, file, cols=1, layout=NULL) {
  library(grid)

  # Make a list from the ... arguments and plotlist
  plots <- c(list(...), plotlist)

  numPlots = length(plots)

  # If layout is NULL, then use 'cols' to determine layout
  if (is.null(layout)) {
    # Make the panel
    # ncol: Number of columns of plots
    # nrow: Number of rows needed, calculated from # of cols
    layout <- matrix(seq(1, cols * ceiling(numPlots/cols)),
                     ncol = cols, nrow = ceiling(numPlots/cols))
  }

  if (numPlots==1) {
    print(plots[[1]])

  } else {
    # Set up the page
    grid.newpage()
    pushViewport(viewport(layout = grid.layout(nrow(layout), ncol(layout))))

    # Make each plot, in the correct location
    for (i in 1:numPlots) {
      # Get the i,j matrix positions of the regions that contain this subplot
      matchidx <- as.data.frame(which(layout == i, arr.ind = TRUE))

      print(plots[[i]], vp = viewport(layout.pos.row = matchidx$row,
                                      layout.pos.col = matchidx$col))
    }
  }
}

qqplot.data <- function (vec) # argument: vector of numbers
{
  # following four lines from base R's qqline()
  y <- quantile(vec[!is.na(vec)], c(0.25, 0.75))
  x <- qnorm(c(0.25, 0.75))
  slope <- diff(y)/diff(x)
  int <- y[1L] - slope * x[1L]
  
  d <- data.frame(resids = vec)
  
  ggplot(d, aes(sample = resids)) + stat_qq(size=0.3) + geom_abline(slope = slope, intercept = int) + theme_bw() + xlab("Theoretical Quantiles") +ylab("Sample Quantiles")
  
}

plot.roc <- function(prediction,output.test) {
  
  perf <- performance(prediction(prediction,output.test), measure="tpr", x.measure="fpr")
  data.plot <- data.frame(x=perf@x.values[[1]],y=perf@y.values[[1]])
  
  p <-   ggplot(data=data.plot) + geom_line(aes(x=x,y=y)) + xlab("False Positive") + ylab("True Positive") + geom_abline(intercept=0,slope=1, linetype="dashed") + theme_bw()
  p
}