plotLength: Plot fragment length profile

In hw538/cfDNAPro: cfDNAPro extracts and Visualises biological features from whole genome sequencing data of cell-free DNA

Plot fragment length profile

Description

Plot fragment length profile

Usage

plotLength(
  x,
  plot_type = c("Fraction"),
  xlim = c(30, 500),
  ylim = NULL,
  x_breaks,
  x_labels,
  vline,
  add_vline = TRUE,
  line_color = "grey1",
  line_size = 0.6,
  line_alpha = 0.8,
  vline_color = "grey",
  vline_type = "dashed",
  vline_size = 0.7,
  area_highlight = NULL,
  output_file = NULL,
  ggsave_params = list(width = 10, height = 11, dpi = 500, bg = "white", unit = "cm"),
  ...
)

Arguments

x	Data to be plotted.
plot_type	Type of plot to generate (e.g., 'count' or 'fraction').
xlim	Limits for the x-axis.
ylim	Limits for the y-axis.
x_breaks	Breaks for the x-axis.
x_labels	Labels for the x-axis.
vline	Position of vertical lines.
add_vline	Logical, whether to add vertical lines.
line_color	Color of the plot lines.
line_size	Size of the plot lines.
line_alpha	Transparency of the plot lines.
vline_color	Color of the vertical lines.
vline_type	Type of the vertical lines (e.g., 'dashed').
vline_size	Size of the vertical lines.
area_highlight	List specifying areas to highlight; each list element is a sublist specifying 'range', 'fill', and 'alpha'.
output_file	File path and name for saving the output plot. Ensure the directory exists and is writable.
ggsave_params	A list of parameters for ggplot2::ggsave(). May include 'width', 'height', 'dpi', etc. Use named elements in the list to specify.
...	Additional parameters for the plotting function.

Value

A ggplot2 object that can be further modified or saved.

Examples

# Assuming 'data' is a dataframe with 'insert_size' and 'value' columns:
plotLength(data, plot_type = "fraction", xlim = c(100, 500), ylim = c(0, 1),
           x_breaks = seq(100, 500, by = 50), add_vline = TRUE, vline = 150)

hw538/cfDNAPro documentation built on Feb. 17, 2025, 6:09 p.m.