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", "T2T", "mm10", "mm9", "ce11"),
  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

# }