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,
  gene_to_highlight = list(ENTREZID = NULL, ENSEMBL = NULL, SYMBOL = c("EGFR", "ERBB2")),
  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),
  ...
)

Arguments

x	QDNAseqCopyNumbers object
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).
...	Other params to geom_txt_repel()

Value

This function returns ggplot2 object.

Author(s)

Haichao Wang

Examples

## Not run: 

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

## End(Not run)

hw538/cfDNAPro documentation built on Aug. 13, 2024, 2:58 p.m.