R/plot_permut_perc_simple.R

In Karpefors/Tendril: Compute and Display Tendril Plots

## Customize permutation plot 2 ( Grey simulated - p.adj actual ) ##
plot_permut_perc_simple <- function(Tendril.perm) {
  Tendril.perm$perm.data[Tendril.perm$perm.data$ang < 0,]$ang <- Tendril.perm$perm.data[Tendril.perm$perm.data$ang < 0,]$ang + 2 * pi
  Tendril.perm$tendril.pi <- TendrilPi(Tendril.perm)

  percentileData <- data.frame(x = Tendril.perm$tendril.pi$x, y = Tendril.perm$tendril.pi$y)
  percentileData$type = Tendril.perm$tendril.pi$type
  percentileData$label = Tendril.perm$tendril.pi$label
  actualData <- data.frame(x = Tendril.perm$data[Tendril.perm$data$Terms == Tendril.perm$Permterm,]$x,
                           y = Tendril.perm$data[Tendril.perm$data$Terms == Tendril.perm$Permterm,]$y,
                           p.adj = Tendril.perm$data[Tendril.perm$data$Terms == Tendril.perm$Permterm,]$p.adj)
  actualData$type="Actual data"
  actualData$label="Actual data"

  cc <- actualData$p.adj
  cc.10 <- log10(cc)
  cc.10[cc.10<(-3)] <- -3
  palette <- tendril_palette()

  element_blank <- ggplot2::element_blank
  aes <- ggplot2::aes
  ggplot2::ggplot(data = Tendril.perm$perm.data,
    aes(x = x, y = y, group = label), aspect = "iso") +
    ggplot2::scale_colour_gradientn(
      colours = palette$grpalette,
      values = palette$values,
      limits = palette$limits
      ) +
    ggplot2::geom_path(colour = "grey80") +
    ggplot2::geom_path(data = percentileData, size = 1, colour = "grey50") +
    ggplot2::geom_path(data = actualData, aes(colour = cc.10), size = 1) +
    ggplot2::geom_point(data = actualData, aes(colour = cc.10), size = 2) +
    ggplot2::coord_fixed(ratio = 1)  +
    ggplot2::theme_bw() +
    ggplot2::theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank()) +
    ggplot2::ggtitle(Tendril.perm$Permterm)
}