Manhattan Plot — ManhattanPlot • ggforge

Creates a Manhattan plot for visualizing genome-wide association study (GWAS) results. This function is adapted from ggmanh::manhattan_plot() with several enhancements:

Parameter names use underscores instead of dots for consistency
chr.colname, pos.colname, pval.colname and label.colname are renamed to chr_by, pos_by, pval_by and label_by
The chromosome and chr.order arguments are merged into chromosomes
The highlight.colname argument is replaced with highlight, which can be a vector of indices or a character expression to select variants, instead of a column name
Point styling controlled by pt_* arguments (size, color, alpha, shape)
Label styling controlled by label_* arguments
Highlight styling controlled by highlight_* arguments
Flexible p-value transformation via pval_transform function
Improved significance threshold handling

Usage

ManhattanPlot(
  data,
  chr_by,
  pos_by,
  pval_by,
  split_by = NULL,
  split_by_sep = "_",
  label_by = NULL,
  chromosomes = NULL,
  pt_size = 0.75,
  pt_color = NULL,
  pt_alpha = alpha,
  pt_shape = 19,
  label_size = 3,
  label_fg = NULL,
  highlight = NULL,
  highlight_color = NULL,
  highlight_size = 1.5,
  highlight_alpha = 1,
  highlight_shape = 19,
  preserve_position = TRUE,
  chr_gap_scaling = 1,
  pval_transform = "-log10",
  signif = c(5e-08, 1e-05),
  signif_color = NULL,
  signif_rel_pos = 0.2,
  signif_label = TRUE,
  signif_label_size = 3.5,
  signif_label_pos = c("left", "right"),
  thin = NULL,
  thin_n = 1000,
  thin_bins = 200,
  rescale = TRUE,
  rescale_ratio_threshold = 5,
  palette = "Dark2",
  palcolor = NULL,
  palreverse = FALSE,
  alpha = 1,
  theme = "theme_ggforge",
  theme_args = list(),
  title = NULL,
  subtitle = NULL,
  xlab = NULL,
  ylab = expression("-" * log[10](p)),
  seed = 8525,
  combine = TRUE,
  nrow = NULL,
  ncol = NULL,
  byrow = TRUE,
  axes = NULL,
  axis_titles = NULL,
  guides = NULL,
  facet_by = NULL,
  design = NULL,
  ...
)

Arguments

data: A data frame or GenomicRanges::GRanges containing the data to be plotted.
chr_by: Column name for chromosome (default: "chr").
pos_by: Column name for position (default: "pos").
pval_by: Column name for p-value (default: "pval").
split_by: Column name(s) to split data into multiple plots
split_by_sep: Separator when concatenating multiple split_by columns
label_by: Column name for the variants to be labeled (default: NULL). Only the variants with non-empty values in this column will be labeled.
chromosomes: A vector of chromosomes to be plotted (default: NULL). If NULL, all chromosomes will be plotted. Can be used to select chromosomes to be plotted or to set the order of the chromosomes.
pt_size: A numeric value to specify the size of the points in the plot.
pt_color: A character string to specify the color of the points in the plot. By default, the color of the points will be controlled by palette or palcolor arguments. This is useful to color the background points when highlight and highlight_color are specified.
pt_alpha: A numeric value to specify the transparency of the points in the plot.
pt_shape: A numeric value to specify the shape of the points in the plot.
label_size: A numeric value to specify the size of the labels in the plot.
label_fg: A character string to specify the color of the labels in the plot. If NULL, the color of the labels will be the same as the points.
highlight: Either a vector of indices or a character expression to select the variants to be highlighted (default: NULL). If NULL, no variants will be highlighted.
highlight_color: A character string to specify the color of the highlighted points.
highlight_size: A numeric value to specify the size of the highlighted points.
highlight_alpha: A numeric value to specify the transparency of the highlighted points.
highlight_shape: A numeric value to specify the shape of the highlighted points.
preserve_position: If TRUE, the width of each chromosome reflects the number of variants and the position of each variant is correctly scaled. If FALSE, the width of each chromosome is equal and the variants are equally spaced.
chr_gap_scaling: A numeric value to specify the scaling of the gap between chromosomes. It is used to adjust the gap between chromosomes in the plot.
pval_transform: A function to transform the p-values (default: "-log10"). If it is a character, it will be evaluated as a function.
signif: A vector of significance thresholds (default: c(5e-08, 1e-05)).
signif_color: A character vector of equal length as signif. It contains colors for the lines drawn at signif. If NULL, the smallest value is colored black while others are grey.
signif_rel_pos: A numeric between 0.1 and 0.9. If the plot is rescaled, where should the significance threshold be positioned?
signif_label: A logical value indicating whether to label the significance thresholds (default: TRUE).
signif_label_size: A numeric value to specify the size of the significance labels.
signif_label_pos: A character string specifying the position of the significance labels. It can be either "left" or "right" (default: "left").
thin: A logical value indicating whether to thin the data (default: NULL). Defaults to TRUE when chromosomes is specified and the length of it is less than the number of chromosomes in the data. Defaults to FALSE otherwise.
thin_n: Number of max points per horizontal partitions of the plot. Defaults to 1000.
thin_bins: Number of bins to partition the data. Defaults to 200.
rescale: A logical value indicating whether to rescale the plot (default: TRUE).
rescale_ratio_threshold: A numeric value to specify the ratio threshold for rescaling.
palette: Color palette name
palcolor: Custom colors for palette
palreverse: A logical value indicating whether to reverse the palette for chromosomes (default: FALSE).
alpha: Transparency level (0-1)
theme: Theme name (string) or theme function
theme_args: List of arguments passed to theme function
title: Plot title
subtitle: Plot subtitle
xlab: X-axis label
ylab: Y-axis label
seed: Random seed for reproducibility
combine: Whether to combine split plots into one
nrow: Number of rows when combining plots
ncol: Number of columns when combining plots
byrow: Fill combined plots by row
axes: How to handle axes in combined plots ("keep", "collect", "collect_x", "collect_y")
axis_titles: How to handle axis titles in combined plots
guides: How to handle guides in combined plots ("collect", "keep", "auto")
facet_by: Column name(s) for faceting the plot
design: Custom layout design for combined plots
...: Additional arguments passed to atomic plotting functions.

Value

A ggplot object or wrap_plots object or a list of ggplot objects. If no split_by is provided, a single plot (ggplot object) will be returned. If 'combine' is TRUE, a wrap_plots object will be returned. If 'combine' is FALSE, a list of ggplot objects will be returned.

Examples

# \donttest{
set.seed(1000)

nsim <- 50000

simdata <- data.frame(
  "chromosome" = sample(c(1:22, "X"), size = nsim, replace = TRUE),
  "position" = sample(1:100000000, size = nsim),
  "P.value" = rbeta(nsim, shape1 = 5, shape2 = 1)^7,
  "cohort" = sample(c("A", "B"), size = nsim, replace = TRUE)
)
simdata$chromosome <- factor(simdata$chromosome, c(1:22, "X"))

if (requireNamespace("ggmanh", quietly = TRUE)) {
  ManhattanPlot(
    simdata,
    pval_by = "P.value", chr_by = "chromosome", pos_by = "position",
    title = "Simulated P.Values", ylab = "P"
  )
}


if (requireNamespace("ggmanh", quietly = TRUE)) {
  # split_by
  ManhattanPlot(
    simdata,
    pval_by = "P.value", chr_by = "chromosome", pos_by = "position",
    title = "Simulated P.Values", ylab = "P", split_by = "cohort", ncol = 1
  )
}


if (requireNamespace("ggmanh", quietly = TRUE)) {
  # Customized p-value transformation and significance threshold line colors
  ManhattanPlot(
    simdata,
    pval_by = "P.value", chr_by = "chromosome", pos_by = "position",
    title = "Simulated -Log2 P.Values", ylab = "-log2(P)", pval_transform = "-log2",
    signif_color = c("red", "blue")
  )
}

# }