plotCNV: plot copy number profile

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

plot copy number profile

Description

plot copy number profile

Usage

plotCNV(
  x,
  frag_obj_mut = NULL,
  gene_to_highlight = list(ENTREZID = NULL, ENSEMBL = NULL, SYMBOL = c("BRAF")),
  genome = "hg19",
  ylim = c(-2, 2),
  chromosome = c(seq(1, 22, 1), "X"),
  point_color = c(Loss = "royalblue", Deletion = "darkblue", Neutral = "darkgrey",
    Amplification = "darkorange", Gain = "orange3"),
  x_title = "Chromosome",
  y_title = "Log2 Ratio",
  point_size = 0.3,
  point_alpha = 0.9,
  chr_edge_color = "black",
  chr_edge_line_size = 0.2,
  chr_edge_alpha = 0.8,
  chr_edge_type = "dotted",
  segment_color = "red",
  segment_alpha = 1,
  segment_line_end = "round",
  segment_line_size = 0.75,
  legend_position = "none",
  x_axis_expand = c(0.1, 0.1),
  y_axis_expand = c(0, 0),
  text_size = 1.6,
  output_file,
  ggsave_params = list(width = 16, height = 4, unit = "cm", dpi = 900),
  ...
)

Arguments

x	QDNAseqCopyNumbers object.
frag_obj_mut	GRanges, optional. A GRanges object containing annotated mutation locus information. If provided, it annotates selected genes with counts of reference and mutant base fragments for specific SNVs within those regions. For detailed analysis instructions and generating a GRanges object, see the 'readBam()' function.
gene_to_highlight	A named list.
genome	string. hg19 or hg38.
ylim	vector. default is c(-2, 2).
chromosome	vector. default is c(seq(1, 22, 1), "X").
point_color	named vector.
x_title	string.
y_title	string.
point_size	numerical. default is 0.3.
point_alpha	numerical. default is 0.9.
chr_edge_color	string. default is "black".
chr_edge_line_size	numerical. default is 0.2.
chr_edge_alpha	numerical. default is 0.8.
chr_edge_type	string. default is "dotted".
segment_color	string. default is "red".
segment_alpha	numerical. default is 1.
segment_line_end	string. default is "round".
segment_line_size	numerical. default is 0.75.
legend_position	string. default is "none", which mean no legends.
x_axis_expand	numerical vector. default is c(0.1, 0.1).
y_axis_expand	numerical vector. default is c(0, 0).
output_file	string, optional Full path and filename for the output plot, including the file extension like ".png" or ".pdf". Ensure the directory exists and is writable.
ggsave_params	A list of parameters to be passed to ggplot2::ggsave(). This list can include any of the arguments that 'ggsave()' accepts. Default settings of 'ggsave()' will be used unless specified. Example: 'list(width = 10, height = 8, dpi = 300)'
...	Other params to geom_txt_repel()

Value

This function returns ggplot2 object.

Author(s)

Haichao Wang, Paulius D. Mennea

Examples

## Not run: 

p <- plotCNV(bamfile = "/path/to/bamfile.bam")

## End(Not run)

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