Violin + box plot for all chromosomes separately (normalized binding counts)

For each chromosome, draws paired violins for two experimental conditions (ex. degron/notag) and compares them with ggpubr::stat_compare_means().

Usage

violin_counts_all_chr(
  object = NULL,
  title = NULL,
  subtitle = NULL,
  ylab = "log2(Normalized binding counts)",
  xlab = NULL,
  conc_condition = "Conc_degron",
  condition_name = "degron",
  conc_baseline = "Conc_notag",
  baseline_name = "notag",
  chr_col = "seqnames",
  chr_of_interest = "chrX",
  ylim = c(0, 12),
  chromosomes = .elegans_chr_order(),
  color_condition = "#ff6347ff",
  color_baseline = "#4682b4ff",
  output_pdf = NULL,
  pdf_width = 14,
  pdf_height = 7
)

Arguments

object

A data.frame or tibble.

title

Character. Main plot title. Default NULL.

subtitle

Character. Plot subtitle. Default NULL.

ylab

Character. Y-axis label. Default log2(Normalized binding counts).

xlab

Character. X-axis label. Default NULL.

conc_condition

Character. Column name for condition counts. Default "Conc_degron".

condition_name

Character. Display name for condition. Default "degron".

conc_baseline

Character. Column name for baseline counts. Default "Conc_notag".

baseline_name

Character. Display name for baseline. Default "notag".

chr_col

Character. Chromosome column name. Default "seqnames".

chr_of_interest

Character. Chromosome to highlight. Default "chrX".

ylim

Numeric vector of length 2. Default c(0, 12).

chromosomes

Character vector. Chromosomes included and their order.

color_condition

Character. Fill colour for condition. Default "#ff6347ff".

color_baseline

Character. Fill colour for baseline. Default "#4682b4ff".

output_pdf

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

pdf_width

Numeric. Default 14.

pdf_height

Numeric. Default 7.

Value

A ggplot2::ggplot object.

Examples

if (FALSE) { # \dontrun{
violin_counts_all_chr(
  object           = my_peaks,
  title            = "Normalized counts per chromosome",
  conc_condition   = "Conc_degron",
  conc_baseline    = "Conc_notag"
)
} # }