A function to generate violin-box plot to compare binding changes (log2FoldChange) between chromosome X and autosomes (A) based on ChIPseq data It also performs a t-test to assess statistical significance.

Usage

violin_log2FC(
  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 = "#4DB6AC",
  ylim = c(-1, 1),
  pvalue_y_position = 0.9
)

Arguments

object: Data frame containing chromosomal and fold change data (diffbind report output)
title: Plot title (optional)
subtitle: Plot subtitle (optional)
ylab: Character. Y-axis label. (default: "log2 Fold Change")
xlab: X-axis label (optional)
log2FC_col: Column name containing log2FoldChange values (default: "Fold")
chr_col: Column name containing chromosome identifiers (default: "seqnames")
chr_of_interest: Chromosome of interest to highlight (default: "chrX")
color_chr_of_interest: Color for chromosome of interest (default: "#EF9A9A")
color_other_chr: Color for other chromosomes (default: "#4DB6AC")
ylim: Y-axis limits (default: c(-1,1))
pvalue_y_position: Vertical position for p-value text (default: 0.9)

Value

A ggplot object containing the violin and box plots

Examples

if (FALSE) { # \dontrun{
# Basic usage with a data frame
violin_box(my_peaks, title = "Expression comparison", ylab = "log2FoldChange")

# Custom chromosome and colors
violin_box(my_peaks, chr_of_interest = "chr1",
          color_chr_of_interest = "red", color_other_chr = "blue")
} # }