Sometimes it is very useful to check details about copy number profile for one or multiple samples. This function is designed to do this job and can be further modified by ggplot2 related packages.
show_cn_profile( data, samples = NULL, show_n = NULL, show_title = FALSE, show_labels = NULL, chrs = paste0("chr", 1:22), position = NULL, genome_build = c("hg19", "hg38", "mm10", "mm9"), ylim = NULL, nrow = NULL, ncol = NULL, return_plotlist = FALSE )
data | a CopyNumber object or a |
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samples | default is NULL, can be a chracter vector representing multiple samples. If |
show_n | number of samples to show, this is used for checking. |
show_title | if |
show_labels | one of |
chrs | chromosomes start with 'chr'. |
position | a position range, e.g. |
genome_build | genome build version, used when |
ylim | limites for y axis. |
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 |
a ggplot
object or a list
# Load copy number object load(system.file("extdata", "toy_copynumber.RData", package = "sigminer", mustWork = TRUE )) p <- show_cn_profile(cn, nrow = 2, ncol = 1) p # \donttest{ p2 <- show_cn_profile(cn, nrow = 2, ncol = 1, position = "chr1:3218923-116319008" ) p2 # }