plot_piano: Generate Piano Plot
In umccr/rock: Rocking R at UMCCR

Description Usage Arguments Value Examples

Generates a piano plot containing copy number variants from multiple samples or callers.

plot_piano(
  cnv_list,
  chromosomes = c(1:22, "X", "Y"),
  hide_x_lab = TRUE,
  seg.col = c("red", "green", "green3", "blue")
)

`cnv_list`	A named list containing one or more `cnv` objects. The element names will be used for plotting the facets so they need to be unique. See the examples for usage.
`chromosomes`	Character vector of chromosomes to plot.
`hide_x_lab`	Boolean. Should the X axis chromosome position labels be hidden or not?
`seg.col`	Character vector of colours to use for deletions, amplifications, extreme amplifications and everything else. Default values: red, green , green3, blue.

A piano plot with copy number variant segments across multiple facets per sample or caller:

X axis: Chromosome Position
Y axis: Total Copy Number
Colour 1 (red): deletions
Colour 2 (light green): amplifications (up to CN6)
Colour 3 (dark green): amplifications (greater than CN6, capped off at CN7)
Colour 4 (blue): everything else

## Not run: 
cnvkit <- system.file("extdata", "HCC2218_cnvkit-call.cns", package = "pebbles")
facets <- system.file("extdata", "HCC2218_facets_cncf.tsv", package = "pebbles")
titan <- system.file("extdata", "HCC2218_titan.segs.tsv", package = "pebbles")
purple <- system.file("extdata", "HCC2218_purple.cnv.tsv", package = "pebbles")
truth <- system.file("extdata", "HCC2218_truthset_cnv_bcbio.tsv", package = "pebbles")

cn_facets <- prep_facets_seg(facets)
cn_cnvkit <- prep_cnvkit_seg(cnvkit)
cn_titan <- prep_titan_seg(titan)
cn_purple <- prep_purple_seg(purple)
cn_truth <- prep_truth_seg(truth)
cnv_list <- list(truth = cn_truth, cnvkit = cn_cnvkit, facets = cn_facets,
                 purple = cn_purple, titan = cn_titan)

plot_piano(cnv_list)
plot_piano(cnv_list, chromosomes = c(1:10))
plot_piano(cnv_list, seg.col = c("orange", "lightblue", "blue", "pink"))

## End(Not run)