Plot CNA profiles from muscadet object

This function generates a multi-panel plot of copy number alteration (CNA) profiles from a muscadet object, including: log R ratios values, log odds ratio (or variant allele frequency), copy numbers, CNA status and cell fractions.

Usage

plotProfile(
  x,
  data,
  title = NULL,
  allelic.type = "lor",
  point.cex = c(0.4, 0.5),
  chrom.colors = c("slategrey", "skyblue"),
  lor.colors = c("peachpuff2", "paleturquoise3"),
  cn.colors = c("grey20", "brown2"),
  cna.colors = c(gain = "#EF6F6AFF", loss = "#6699CCFF", cnloh = "#44AA99FF"),
  cf.colors = c("white", "grey20", "bisque2"),
  dipLogR.color = c("magenta4"),
  seg.color = c("brown2")
)

Arguments

x

A muscadet object containing CNA calling data to be visualized (generated using cnaCalling()).

data

Either a cluster identifier to plot data of a cluster or "allcells" to plot data on all cells.

title

An optional title for the plot. Default is NULL.

allelic.type

A character string indicating the allelic metric to plot: "lor" for log odds ratio or "vaf" for variant allele frequency. Default is "lor".

point.cex

Numeric vector of length 1 or 2 specifying the size of points in the plots. If a single value is provided, it will be replicated for both plots. Default is c(0.4, 0.5).

chrom.colors

A character vector of length 2 defining alternating chromosome colors. Default is c("slategrey", "skyblue").

lor.colors

A character vector of length 2 for log odds ratio point colors depending of variant allele frequency in all cells. Use "none" to use the alternating chromosome colors (defined by chrom.colors). Default is c("peachpuff2", "paleturquoise3").

cn.colors

A character vector of length 2 for total copy number and minor allele copy number segment colors. Default is c("black", "brown2").

cna.colors

A vector of 3 colors for CNA states: gain, loss, and cnloh (or named vector where names are "gain", "loss", and "cnloh" and the values are their respective colors). Default is c("gain" = "#EF6F6AFF", "loss" = "#6699CCFF", "cnloh" = "#44AA99FF").

cf.colors

A character vector of length 3 for cellular fraction gradient (of 10 values): start color of the gradient, end color of the gradient, and color for normal diploid (depending on the ploidy). Default is c("white", "steelblue", "bisque2").

dipLogR.color

A character string for the diploid log R ratio line color. Default is "magenta4".

seg.color

A character string for the color of segment medians. Default is "brown2".

Value

A multi-panel plot of CNA profiles is produced.

Examples

if (FALSE) { # \dontrun{
# Load example muscadet object
# data("muscadet_obj")

# Plot profile for all cells
pdf("CNAprofile_allcells.pdf", width = 15, height = 7.5) # Save as PDF
plotProfile(muscadet_obj, data = "allcells", title = "Example data - all cells")
dev.off()
} # }