Creates violin-box plots to compare normalized binding counts values between different conditions and chromosomes, typically comparing X chromosome vs autosomes.

Usage

violin_counts(
  object = NULL,
  title = NULL,
  subtitle = NULL,
  ylab = NULL,
  xlab = NULL,
  conc_condition = "Conc_degron",
  condition_name = "degron",
  conc_baseline = "Conc_notag",
  baseline_name = "notag",
  chr_col = "seqnames",
  chr_of_interest = "chrX",
  label.y_plot = c(9, 10, 11, 12),
  ylim = c(0, 12),
  colors = c("#4682b4ff", "#ff6347ff", "#4682b4ff", "#ff6347ff"),
  pvalue_y_position = 1.5
)

Arguments

object: Data frame containing chromosomal and normalized binding counts, concentration from diffbind report output.
title: Plot title
subtitle: Plot subtitle
ylab: Y-axis label (if NULL, a default will be created)
xlab: X-axis label
conc_condition: Column name for condition concentration values
condition_name: Name to use for the condition in labels
conc_baseline: Column name for baseline concentration values
baseline_name: Name to use for the baseline in labels
chr_col: Column name containing chromosome information
chr_of_interest: Chromosome of interest to separate (e.g., "chrX")
label.y_plot: Y positions for statistical test labels
ylim: Y-axis limits
colors: Vector of colors for the different groups
pvalue_y_position: Y position for sample size labels

Value

A ggplot object containing the violin and box plots

Examples

# Example usage:
# violin_box_conc(df, title = "Concentration Comparison", chr_of_interest = "chrX")