R/plot_permutation.R

In AstraZeneca/Tendril: Compute and Display Tendril Plots

plot_permutation <- function(x, coloring){
  #prepare data
  perm.data <- x$perm.data
  dataset <- x$tendril$data
  data <- dataset[dataset$Terms == unique(perm.data$Terms),]

  #get data from actual and permutations and bind together
  actualdata <- createDataset(data$x, data$y, "Actual", "Actual", data$StartDay, perm.data)
  actualdata$color<-data[[coloring]]
  plotdata <- createDataset(perm.data$x, perm.data$y, perm.data$label, perm.data$type, perm.data$StartDay, perm.data)
  plotdata$color<-NA
  plotdata<- rbind(actualdata, plotdata)

  if (coloring %in% LOG_COLORING_OPTIONS) {
    plotdata$color<-pmax(log10(plotdata$color), -3)
  }
  palette <- tendril_palette()

  #plot parameters
  Title <- paste(unique(perm.data$Terms), ", from day: ", unique(plotdata$perm.from.day), sep = "")
  data2.labels <- data.frame(
    xpos = c(Inf, -Inf),
    ypos = c(Inf, Inf),
    label = x$tendril$Treatments,
    hjust = c(1,0),
    vjust = c(1,1)
  )

  y<-NULL
  label<-NULL
  type<-NULL
  aes <- ggplot2::aes
  element_blank <- ggplot2::element_blank

  p<-ggplot2::ggplot(data=plotdata[plotdata$type=="Permutation", ], aes(x=x, y=y, group=label), aspect="iso")
  if (coloring %in% LOG_COLORING_OPTIONS) {
    p <- p +
      ggplot2::scale_colour_gradientn("log(p-val)",
        colours=palette$grpalette,
        values = palette$values,
        limits = palette$limits
      )
  } else if (coloring != "Terms") {
    p <- p + ggplot2::scale_colour_gradient(coloring)
  }
  p <- p + ggplot2::geom_path(color = "Grey80")
  if (coloring!="Terms") {
    p <- p +
      ggplot2::geom_path(data=plotdata[plotdata$type=="Actual", ], aes(x=x, y=y, group=label, color = color))+
      ggplot2::geom_point(data=plotdata[plotdata$type=="Actual", ], aes(x=x, y=y, group=label, color = color), size=2)
  } else {
    p <- p +
      ggplot2::geom_path(data=plotdata[plotdata$type=="Actual", ], aes(x=x, y=y, group=label), color = "blue")+
      ggplot2::geom_point(data=plotdata[plotdata$type=="Actual", ], aes(x=x, y=y, group=label), color = "blue", size=2)
  }
  p <- p +
    ggplot2::theme_bw() +
    ggplot2::theme(axis.title.x = element_blank(),
          axis.text.x = element_blank(),
          axis.ticks.x = element_blank(),
          axis.title.y = element_blank(),
          axis.text.y = element_blank(),
          axis.ticks.y = element_blank()) +
    ggplot2::theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank()) +
    ggplot2::labs(color = "Type") +
    ggplot2::coord_fixed(ratio=1) +
    ggplot2::ggtitle(Title) +
    ggplot2::annotate(geom="text", x=data2.labels$xpos, y=data2.labels$ypos,
               label = data2.labels$label,
               hjust=data2.labels$hjust, vjust=data2.labels$vjust,
               colour = "grey40", size = 5, fontface = 2)

  return(p)

}