plot_xy_with_ploidy_guides: Plot X–Y scatter with ploidy dosage guide lines and optional...

In Qploidy: Estimation of Ploidy and Detection of Aneuploidy Using Genotyping Data

Plot X–Y scatter with ploidy dosage guide lines and optional sample highlighting

Description

Creates a dot plot of allele counts 'X' (A-allele) vs 'Y' (B-allele) and overlays expected dosage guide lines for a given ploidy. You can either color all samples ('sample = "all"') or highlight a single sample while rendering the others in gray. Samples that have no plotted points (e.g., due to non-finite 'X'/'Y') are automatically omitted from the legend.

Usage

plot_xy_with_ploidy_guides(
  df,
  ploidy = 2,
  sample = NULL,
  highlight_color = "tomato",
  other_color = "grey75"
)

Arguments

df	A 'data.frame' containing at least columns 'X' and 'Y'. If 'sample = "all"' or a specific sample is to be highlighted, 'df' should also contain a 'SampleName' column.
ploidy	Integer (>= 2). Ploidy used to compute and draw dosage guide lines.
sample	Character. Either '"all"' to color all samples by 'SampleName', or the name of a single sample to highlight. Default: '"all"'.
highlight_color	Color used for the highlighted sample when 'sample != "all"'. Default: '"tomato"'.
other_color	Color used for non-highlighted samples when 'sample != "all"'. Default: '"grey75"'.

Details

The function: * Drops rows where 'X' or 'Y' are non-finite before plotting and builds the legend from the remaining points. * When 'sample = "all"', colors points by 'SampleName' (requires a 'SampleName' column). * When 'sample' is a specific name, only that sample is colored with 'highlight_color'; all others use 'other_color'. If the requested sample has no plotted points, it is omitted from the legend. * Draws dosage guide lines for dosages 'd = 0, …, ploidy': 'd = 0' → horizontal line 'Y = 0'; 'd = ploidy' → vertical line 'X = 0'; intermediate dosages are lines through the origin with slope (d/ploidy) / (1 - d/ploidy). * Uses a fixed aspect ratio ('coord_fixed') so that one unit on the x- and y-axes has the same length.

Value

A **ggplot** object.

See Also

[plot_baf_with_ploidy_guides()] for plotting standardized BAF-based coordinates.

Qploidy documentation built on July 11, 2026, 5:06 p.m.