Show Summary Copy Number Profile for Sample Groups

show_cn_group_profile(
  data,
  groups = NULL,
  fill_area = TRUE,
  cols = NULL,
  chrs = paste0("chr", c(1:22, "X")),
  genome_build = c("hg19", "hg38", "mm10", "mm9"),
  cutoff = 2L,
  resolution_factor = 1L,
  force_y_limit = TRUE,
  highlight_genes = NULL,
  repel = FALSE,
  nrow = NULL,
  ncol = NULL,
  return_plotlist = FALSE
)

Arguments

data	a `CopyNumber` object or a data.frame containing at least 'chromosome', 'start', 'end', 'segVal', 'sample' these columns.
groups	a named list or a column name for specifying groups.
fill_area	default is `TRUE`, fill area with colors.
cols	length-2 colors for AMP and DEL.
chrs	chromosomes start with 'chr'.
genome_build	genome build version, used when `data` is a `data.frame`, should be 'hg19' or 'hg38'.
cutoff	copy number value cutoff for splitting data into AMP and DEL. The values equal to cutoff are discarded. Default is `2`, you can also set a length-2 vector, e.g. `c(2, 2)`.
resolution_factor	an integer to control the resolution. When it is `1` (default), compute frequency in each cytoband. When it is `2`, use compute frequency in each half cytoband.
force_y_limit	default is `TRUE`, force multiple plots
highlight_genes	gene list to highlight. have same y ranges. You can also set a length-2 numeric value.
repel	if `TRUE` (default is `FALSE`), repel highlight genes to avoid overlap.
nrow	number of rows in the plot grid when multiple samples are selected.
ncol	number of columns in the plot grid when multiple samples are selected.
return_plotlist	default is `FALSE`, if `TRUE`, return a plot list instead of a combined plot.

Value

a (list of) ggplot object.

Examples

load(system.file("extdata", "toy_copynumber.RData",
  package = "sigminer", mustWork = TRUE
))

p1 <- show_cn_group_profile(cn)
p1
# \donttest{
ss <- unique(cn@data$sample)
p2 <- show_cn_group_profile(cn, groups = list(a = ss[1:5], b = ss[6:10]))
p2
p3 <- show_cn_group_profile(cn,
  groups = list(g1 = ss[1:5], g2 = ss[6:10]),
  force_y_limit = c(-1, 1), nrow = 2
)
p3

## Set custom cutoff for custom data
data <- cn@data
data$segVal <- data$segVal - 2L
p4 <- show_cn_group_profile(data,
  groups = list(g1 = ss[1:5], g2 = ss[6:10]),
  force_y_limit = c(-1, 1), nrow = 2,
  cutoff = c(0, 0)
)
p4

## Add highlight gene
p5 <- show_cn_group_profile(cn, highlight_genes = c("TP53", "EGFR"))
p5
# }