all_resolutions_plots: Plot graphics for ploidy visual inspection for each...

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

Plot graphics for ploidy visual inspection for each resolution

Description

This function generates and saves plots for visual inspection of ploidy at different resolutions: chromosome, chromosome-arm, and sample levels. It is designed for parallelization purposes and supports customization of centromere positions and chromosome selection.

Usage

all_resolutions_plots(
  data_standardized,
  sample,
  ploidy,
  centromeres,
  types_chromosome = c("Ratio_hist", "BAF_hist", "zscore"),
  types_chromosome_arm = c("Ratio_hist", "BAF_hist", "zscore"),
  types_sample = c("Ratio_hist_overall", "BAF_hist_overall"),
  file_name = NULL,
  chr = NULL
)

Arguments

data_standardized	An object of class 'qploidy_standardization' containing standardized data for ploidy analysis.
sample	A character string specifying the sample name to be analyzed.
ploidy	A numeric value indicating the expected ploidy of the sample. This parameter is required.
centromeres	A named vector with centromere positions (in base pairs) for each chromosome. The names must match the chromosome IDs in the dataset. This is used for chromosome-arm level resolution.
types_chromosome	A character vector defining the plot types for chromosome-level resolution. Options include: - "het": Plots heterozygous locus counts. - "BAF": Plots B-allele frequency (BAF). - "zscore": Plots z-scores. - "BAF_hist": Plots BAF histograms for each chromosome. - "ratio": Plots raw ratios for each chromosome. Default is c("Ratio_hist", "BAF_hist", "zscore").
types_chromosome_arm	A character vector defining the plot types for chromosome-arm level resolution. Options include: - "het": Plots heterozygous locus counts. - "BAF": Plots B-allele frequency (BAF). - "zscore": Plots z-scores. - "BAF_hist": Plots BAF histograms for each chromosome arm. - "ratio": Plots raw ratios for each chromosome arm. Default is c("Ratio_hist", "BAF_hist", "zscore").
types_sample	A character vector defining the plot types for sample-level resolution. Options include: - "Ratio_hist_overall": Plots a histogram of raw ratios for the entire genome. - "BAF_hist_overall": Plots a BAF histogram for the entire genome. Default is c("Ratio_hist_overall", "BAF_hist_overall").
file_name	A character string defining the output file path and name prefix for the saved plots. The function appends resolution-specific suffixes to this prefix. If NULL, plots are not saved to files.
chr	A vector specifying the chromosomes to include in the analysis. If NULL, all chromosomes are included.

Details

The function generates three types of plots:

- **Chromosome-level resolution**: Plots raw ratio, BAF histograms, z-scores, heterozygous locus counts, and BAF for each chromosome. - **Chromosome-arm level resolution**: Similar to chromosome-level but splits data by chromosome arms using centromere positions. - **Sample-level resolution**: Combines all markers in the sample to generate overall raw ratio and BAF histograms.

The plots are saved as PNG files with the following suffixes: - '_res:chromosome.png' - '_res:chromosome_arm.png' - '_res:sample.png'

If 'file_name' is NULL, the plots are not saved to files but are returned in the output list.

Value

A list containing the generated plots for each resolution: - 'chromosome': Plot for chromosome-level resolution. - 'chromosome_arm': Plot for chromosome-arm level resolution (if centromeres are provided). - 'sample': Plot for sample-level resolution.

Qploidy documentation built on June 8, 2025, 10 a.m.