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Violin + box plot for all chromosomes separately (log2 fold change)

Source: R/violin_all_chr.R
violin_log2FC_all_chr.Rd

Draws one violin + boxplot per chromosome and compares each autosome against the chromosome of interest using ggpubr::stat_compare_means().

Usage

violin_log2FC_all_chr(
  object = NULL,
  title = NULL,
  subtitle = NULL,
  ylab = "log2 Fold Change",
  xlab = NULL,
  log2FC_col = "Fold",
  chr_col = "seqnames",
  chr_of_interest = "chrX",
  color_chr_of_interest = "#EF9A9A",
  color_other_chr = c("#4DB6AC", "#4DB6AC", "#4DB6AC", "#4DB6AC", "#4DB6AC"),
  ylim = c(-2, 2),
  chromosomes = .elegans_chr_order(),
  output_pdf = NULL,
  pdf_width = 12,
  pdf_height = 6
)

Arguments

object

A data.frame or tibble from DiffBind::dba.report().

title

Character. Main plot title. Default NULL.

subtitle

Character. Plot subtitle. Default NULL.

ylab

Character. Y-axis label. Default log2 Fold Change.

xlab

Character. X-axis label. Default NULL.

log2FC_col

Character. Column name for log2 fold-change. Default "Fold".

chr_col

Character. Column name for chromosome identifiers. Default "seqnames".

chr_of_interest

Character. Chromosome to highlight. Default "chrX".

color_chr_of_interest

Character. Fill colour for chrX. Default "#EF9A9A".

color_other_chr

Character. Fill colour for autosomes. Default "#4DB6AC".

ylim

Numeric vector of length 2. Y-axis limits. Default c(-2, 2).

chromosomes

Character vector. Chromosomes to include and their order. Default is C. elegans order: c("chrI","chrII","chrIII","chrIV","chrV","chrX").

output_pdf

Character. Optional path to save plot as PDF. Default NULL.

pdf_width

Numeric. PDF width in inches. Default 12.

pdf_height

Numeric. PDF height in inches. Default 6.

Value

A ggplot2::ggplot object.

Examples

if (FALSE) { # \dontrun{
violin_log2FC_all_chr(
  object          = my_peaks,
  title           = "log2FC per chromosome",
  chr_of_interest = "chrX",
  ylim            = c(-2, 2)
)
} # }