Declare that a point layer draws a Manhattan plot

maidr_manhattan() is ggplot2::geom_point() with three things added: the author saying that the points are a Manhattan plot, the significance threshold the chart is read against, and two aesthetics for what each point is – label (the SNP or variant) and region (its chromosome). A declared layer is read as a manhattan: the description says how many points clear the threshold and names them, a rotor mode steps through only those points, and every point is announced with its label and chromosome. The same points drawn with geom_point() read as a scatter of tens of thousands of positions, walked one at a time.

Nothing about the picture changes: the geom draws exactly what geom_point() draws, and neither label nor region reaches a mark.

The manhattan layer type [experimental] is one of the experimental plot types: it has not been through a user study, and its reading may change without a deprecation period. See "Experimental Plot Types" in the README.

Usage

maidr_manhattan(
  mapping = NULL,
  data = NULL,
  position = "identity",
  ...,
  significance,
  direction = c("above", "below"),
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE
)

Arguments

mapping: Aesthetics, as for ggplot2::geom_point(): x (the position along the genome) and y (the significance, such as -log10 of the p value) are required. label may name each point (the SNP) and region its chromosome; both are announced with the point. Every other point aesthetic (colour, size, alpha, ...) behaves exactly as it does there.
data: The layer's data, as for ggplot2::geom_point().
position: Position adjustment, as for ggplot2::geom_point().
...: Other arguments passed to the layer, as for ggplot2::geom_point() – except stat, which is fixed at "identity": a declared layer is always drawn from the author's own points.
significance: The significance cutoff on the y axis, one number in the units y is announced in. Required.
direction: Which side of significance the significant points are on: "above" (the default) for a -log10(p) axis, "below" for a raw p value.
na.rm: If FALSE (the default), rows with missing values are removed with a warning.
show.legend: Whether this layer is included in the legends.
inherit.aes: If FALSE, the plot's default aesthetics are not inherited.

Value

A ggplot2 layer, to be added to a plot with +.

Details

x is the position along the genome – usually each variant's position offset by the length of the chromosomes before it, with the axis labelled by chromosome through scale_x_continuous(breaks = , labels = ) – and y the significance. A point is significant when its y is at or above significance (at or below it with direction = "below"), in the units y is announced in: significance = -log10(5e-8) for genome-wide significance on a -log10(p) axis. There is no default, for the reason maidr_volcano() gives.

Examples

if (requireNamespace("ggplot2", quietly = TRUE)) {
  snps <- data.frame(
    snp = paste0("rs", 1:8),
    chr = rep(c("1", "2"), each = 4),
    pos = c(1, 2, 3, 4, 6, 7, 8, 9),
    p = c(0.3, 2e-9, 0.01, 0.6, 0.05, 0.8, 4e-10, 0.2)
  )

  manhattan <- ggplot2::ggplot(
    snps,
    ggplot2::aes(x = pos, y = -log10(p), colour = chr)
  ) +
    maidr_manhattan(
      ggplot2::aes(label = snp, region = chr),
      significance = -log10(5e-8)
    ) +
    ggplot2::geom_hline(yintercept = -log10(5e-8), linetype = "dashed") +
    ggplot2::scale_x_continuous(breaks = c(2.5, 7.5), labels = c("1", "2")) +
    ggplot2::labs(x = "Chromosome", y = "-log10 p")

  if (interactive()) {
    show(manhattan)
  }
}