ggseqlogo2: Quick sequence logo plot

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

Quick sequence logo plot

Description

ggseqlogo is a shortcut for generating sequence logos. It adds the ggseqlogo theme theme_logo by default, and facets when multiple input data are provided. It serves as a convenient wrapper, so to customise logos beyond the defaults here, please use geom_logo.

Usage

ggseqlogo2(
  data,
  facet = "wrap",
  scales = "free_x",
  ncol = NULL,
  nrow = NULL,
  idor = NULL,
  ...
)

geom_logo2(
  data = NULL,
  method = "bits",
  seq_type = "auto",
  namespace = NULL,
  font = "roboto_medium",
  stack_width = 0.95,
  rev_stack_order = F,
  col_scheme = "auto",
  low_col = "black",
  high_col = "yellow",
  na_col = "grey20",
  plot = TRUE,
  idor = NULL,
  ...
)

Arguments

data	Character vector of sequences or named list of sequences. All sequences must have same width
facet	Facet type, can be 'wrap' or 'grid'
scales	Facet scales, see facet_wrap
ncol	Number of columns, works only when facet='wrap', see facet_wrap
nrow	Number of rows, same as ncol
idor	a named vector (like a dictory) to change letters one to one in the plot.
...	Additional arguments passed to geom_logo
method	Height method, can be one of "bits" or "probability" (default: "bits")
seq_type	Sequence type, can be one of "auto", "aa", "dna", "rna" or "other" (default: "auto", sequence type is automatically guessed)
namespace	Character vector of single letters to be used for custom namespaces. Can be alphanumeric, including Greek characters.
font	Name of font. See list_fonts for available fonts.
stack_width	Width of letter stack between 0 and 1 (default: 0.95)
rev_stack_order	If TRUE, order of letter stack is reversed (default: FALSE)
col_scheme	Color scheme applied to the sequence logo. See list_col_schemes for available fonts. (default: "auto", color scheme is automatically picked based on seq_type). One can also pass custom color scheme objects created with the make_col_scheme function
low_col	Colors for low and high ends of the gradient if a quantitative color scheme is used (default: "black" and "yellow").
high_col	Colors for low and high ends of the gradient if a quantitative color scheme is used (default: "black" and "yellow").
na_col	Color for letters missing in color scheme (default: "grey20")
plot	If FALSE, plotting data is returned

Examples

library(ggseqlogo)
data(ggseqlogo_sample)

## Same as ggseqlogo()
p1 <- ggseqlogo2(seqs_dna[[1]])
p1

## Extra feature
idor <- as.character(1:4)
names(idor) <- c("A", "C", "G", "T")
p2 <- ggseqlogo2(seqs_dna[[1]], idor = idor)
p2

ShixiangWang/CNVMotif documentation built on June 3, 2022, 3:44 a.m.