ggseqlogo (version 0.2)

geom_logo: Plots sequence logo as a layer on ggplot

Description

Plots sequence logo as a layer on ggplot

Usage

geom_logo(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 = T, ...)

Arguments

data

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")

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, 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

...

Additional arguments passed to layer params

Examples

# Load sample data
data(ggseqlogo_sample)

# Produce single sequence logo using geom_logo
p1 = ggseqlogo( seqs_dna[[1]] )