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"),
  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
# }