Package 'ggseqlogo'

Title: A 'ggplot2' Extension for Drawing Publication-Ready Sequence Logos
Description: The extensive range of functions provided by this package makes it possible to draw highly versatile sequence logos. Features include, but not limited to, modifying colour schemes and fonts used to draw the logo, generating multiple logo plots, and aiding the visualisation with annotations. Sequence logos can easily be combined with other plots 'ggplot2' plots.
Authors: Omar Wagih
Maintainer: Omar Wagih <[email protected]>
License: LGPL
Version: 0.2
Built: 2024-10-06 06:24:13 UTC
Source: CRAN

Help Index


List color schemes available in ggseqlogo

Description

List color schemes available in ggseqlogo

Usage

list_col_schemes(v = T)

Arguments

v

If true, font names are printed to stderr. Otherwise, color scheme names are returned as a character vector


List fonts available in ggseqlogo

Description

List fonts available in ggseqlogo

Usage

list_fonts(v = T)

Arguments

v

If true, font names are printed to stderr. Otherwise, font names are returned as a character vector


Create new sequence logo color scheme

Description

Create new sequence logo color scheme

Usage

make_col_scheme(chars = NULL, groups = NULL, cols = NULL, values = NULL,
  name = "")

Arguments

chars

Vector of one letter characters

groups

Vector of groups for letters with same length as chars (optional if cols parameter is provided)

cols

Vector of colors with same length as chars (optional if values parameter is provided)

values

Vector of numerical values with same length as chars

name

Name of color scheme

Examples

# Discrete color scheme examples
cs1 = make_col_scheme(chars=c('A', 'T', 'G', 'C'), groups=c('g1', 'g1', 'g2', 'g2'), 
                      cols=c('red', 'red', 'blue', 'blue'), name='custom1')

cs2 = make_col_scheme(chars=c('A', 'T', 'G', 'C'), cols=c('red', 'red', 'blue', 'blue'), 
                      name='custom2')

# Quantitative color scheme
cs3 = make_col_scheme(chars=c('A', 'T', 'G', 'C'), values=1:4, name='custom3')

List of position frequency matrices for transcription factors

Description

List of position frequency matrices for transcription factors


List of aligned kinase-substrate binding sequences

Description

List of aligned kinase-substrate binding sequences


List of aligned transcription factor binding sequences

Description

List of aligned transcription factor binding sequences