plotCNV: plot copy number profile

View source: R/plotCNV.R

plotCNVR Documentation

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.