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.
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
)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.
An object of class `qploidy_standardization` containing standardized data for ploidy analysis.
A character string specifying the sample name to be analyzed.
A numeric value indicating the expected ploidy of the sample. This parameter is required.
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.
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").
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").
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").
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.
A vector specifying the chromosomes to include in the analysis. If NULL, all chromosomes are included.
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.