show_seq_logo: Show Copy Number Sequence Logos

In ShixiangWang/sigminer.helper: Explore, Analyze and Visualize Catalogs and Patterns of Copy Number Variation in Cancer Genomics

Show Copy Number Sequence Logos

Description

Show Copy Number Sequence Logos

Usage

show_seq_logo(
  x,
  method = c("prob", "bits"),
  simple_version = FALSE,
  ncol = NULL,
  nrow = NULL,
  recode = FALSE,
  indicator = NULL,
  ...
)

Arguments

x	a character vector of sequences or named list of sequences. All sequences must have same width.
method	Height method, can be one of "bits" or "probability" (default: "bits")
simple_version	if TRUE, just use segmental copy number value.
ncol	Number of columns, works only when facet='wrap', see facet_wrap
nrow	Number of rows, same as ncol
recode	if TRUE, it will use default indicator or specified indicator to show the letters in the plot
indicator	a named vector (like a dictory) to change letters one to one in the plot.
...	Additional arguments passed to geom_logo

Value

a ggplot object

Examples

p1 <- show_seq_logo(sapply(split(LETTERS[1:24], 1:4), function(x) paste0(x, collapse = "")))
p1
p2 <- show_seq_logo(sapply(split(LETTERS[1:24], 1:4), function(x) paste0(x, collapse = "")),
  recode = TRUE
)
p2
p3 <- show_seq_logo(sapply(split(LETTERS[1:6], 1:2), function(x) paste0(x, collapse = "")),
  simple_version = TRUE
)

ShixiangWang/sigminer.helper documentation built on May 22, 2022, 6:05 a.m.