plot_qploidy_standardization: Plot Method for Qploidy Standardization
In Qploidy: Estimation of Ploidy and Detection of Aneuploidy Using Genotyping Data

plot_qploidy_standardization

R Documentation

Plot Method for Qploidy Standardization

Description

This function generates various plots for visualizing the results of Qploidy standardization. It supports multiple plot types, including BAF, z-score, and histograms.

Usage

plot_qploidy_standardization(
  x,
  sample = NULL,
  chr = NULL,
  type = c("all", "het", "BAF", "zscore", "BAF_hist", "ratio", "BAF_hist_overall",
    "Ratio_hist_overall"),
  area_single = 0.75,
  ploidy = 4,
  dot.size = 1,
  font_size = 12,
  add_estimated_peaks = FALSE,
  add_expected_peaks = FALSE,
  centromeres = NULL,
  add_centromeres = FALSE,
  colors = FALSE,
  window_size = 2e+06,
  het_interval = 0.1,
  rm_homozygous = FALSE,
  ...
)

Arguments

`x`	An object of class 'qploidy_standardization'.
`sample`	Character string indicating the sample ID to plot.
`chr`	Character or numeric vector specifying the chromosomes to plot. Default is NULL (plots all chromosomes).
`type`	Character vector defining the plot types. Options include: - "all": Generates all available plot types. - "het": Plots heterozygous locus counts across genomic windows. - "BAF": Plots B-allele frequency (BAF) for each chromosome. - "zscore": Plots z-scores for each chromosome. - "BAF_hist": Plots BAF histograms for each chromosome. - "BAF_hist_overall": Plots a BAF histogram for the entire genome. - "Ratio_hist_overall": Plots a histogram of raw ratios for the entire genome. - "ratio": Plots raw ratios for each chromosome. Default is "all".
`area_single`	Numeric value defining the area around the expected peak to be considered. Default is 0.75.
`ploidy`	Integer specifying the expected ploidy. Default is 4.
`dot.size`	Numeric value for the size of the dots in the plots. Default is 1.
`font_size`	Numeric value for the font size of plot labels. Default is 12.
`add_estimated_peaks`	Logical. If TRUE, adds lines for estimated peaks. Default is FALSE.
`add_expected_peaks`	Logical. If TRUE, adds lines for expected peaks. Default is FALSE.
`centromeres`	Named vector defining centromere positions for each chromosome. Names must match chromosome IDs in 'x'.
`add_centromeres`	Logical. If TRUE, adds vertical lines at centromere positions. Default is FALSE.
`colors`	Logical. If TRUE, adds area colors to the plots. Default is FALSE.
`window_size`	Numeric value defining the genomic position window for heterozygous locus counts. Default is 2000000.
`het_interval`	Numeric value defining the interval to consider as heterozygous. Default is 0.1.
`rm_homozygous`	Logical. If TRUE, removes homozygous calls from BAF histogram plots. Default is FALSE.
`...`	Additional plot parameters.

Details

The function supports the following plot types:

- **all**: Generates all available plot types. - **het**: Plots the proportion of heterozygous loci across genomic windows, useful for identifying regions with high or low heterozygosity. - **BAF**: Plots the B-allele frequency (BAF) for each chromosome, showing the distribution of allele frequencies. - **zscore**: Plots z-scores for each chromosome, which can help identify outliers or regions with unusual data distributions. - **BAF_hist**: Plots histograms of BAF values for each chromosome, providing a summary of allele frequency distributions. - **BAF_hist_overall**: Plots a single histogram of BAF values for the entire genome, summarizing allele frequency distributions genome-wide. - **Ratio_hist_overall**: Plots a histogram of raw ratios for the entire genome, useful for visualizing overall ratio distributions. - **ratio**: Plots raw ratios for each chromosome, showing the distribution of observed ratios.