weblogo: Plot a sequence logo

Description

This function will plot a sequence logo given aligned sequences. For more details on the parameters, see the WebLogo user manual at http://weblogo.threeplusone.com/manual.html

Usage

weblogo(seqs, file.in, open = TRUE, verbose = TRUE, return.cmd = F, datatype = "plain", file.out, format = "pdf", sequence.type = "protein", alphabet, units = "bits", composition = "auto", weight, first.index, lower, upper, ignore.lower.case = TRUE, reverse, complement, size = "large", stacks.per.line = 40, title, label, show.xaxis = TRUE, xlabel, annotate, yaxis, show.yaxis = TRUE, ylabel, show.ends = FALSE, fineprint = "", ticmarks = 1, errorbars = FALSE, reverse.stacks = TRUE, color.scheme = "auto", stack.width = 10.8, aspect.ratio = 5, box = FALSE, resolution = 300, scale.width = TRUE, rotate.numbers = FALSE, hide.tics = FALSE)

Arguments

seqs

Aligned sequences as an R character vector. Sequences must all have the same length. Alternatively, you can provide a file containing your sequence alignment using file.in.

file.in

A file containing your sequence alignment in one of the following formats: clustal, fasta, plain, msf, genbank, nbrf, nexus, phylip, stockholm, intelligenetics, table, array, transfac. This file is only to be provided if you are not inputting data with 'seqs'. To set your data format, see the datatype option.

open

Open the generated logo file? (default: TRUE).

verbose

Write status messages to the R console? (default: TRUE).

return.cmd

Logical indicating if RWebLogo should return the WebLogo command generated (default: FALSE).

datatype

Type of multiple sequence alignment or position weight matrix file: ('clustal', 'fasta','plain', 'msf', 'genbank', 'nbrf', 'nexus', 'phylip', 'stockholm', 'intelligenetics', 'table', 'array', 'transfac'). You usually don't need to specify this, as weblogo will try figure out the format of your file.

file.out

Output file. For example, /path/to/dir/mylogo.pdf. By default this is your working directory + RWebLogo. + selected format.

format

Format of output: 'pdf' (default) 'eps', 'png', 'jpeg', 'svg'.

sequence.type

The type of sequence data: 'protein', 'rna' or 'dna'.

alphabet

The set of symbols to count, e.g. 'AGTC'. All characters not in the alphabet are ignored. If neither the alphabet nor sequence-type are specified then weblogo will examine the input data and make an educated guess.

units

A unit of entropy ('bits' (default), 'nats', 'digits'), or a unit of free energy ('kT', 'kJ/mol', 'kcal/mol'), or 'probability' for probabilities.

composition

The expected composition of the sequences: 'auto' (default), 'equiprobable', 'none' (do not perform any compositional adjustment), a CG percentage, a species name ('H. sapiens', 'E. coli', 'S. cerevisiae', 'C. elegans', 'D. melanogaster', 'M. musculus', 'T. thermophilus'), or an explicit distribution as a named numerical vector (e.g. c(A=10, C=40, G=40, T=10)). The automatic option uses a typical distribution for proteins and equiprobable distribution for everything else.

weight

The weight of prior data. Default depends on alphabet length.

first.index

Index of first position in sequence data (default: 1).

lower

Lower bound index of sequence to display.

upper

Upper bound index of sequence to display.

ignore.lower.case

Disregard lower case letters and only count upper case letters in sequences.

reverse

reverse sequences.

complement

complement DNA sequences.

size

Specify a standard logo size: 'small', 'medium', 'large' (default).

stacks.per.line

Maximum number of logo stacks per logo line (default: 40).

title

Logo title text.

label

A figure label, e.g. '2a'.

show.xaxis

Display sequence numbers along x-axis? (default: TRUE).

xlabel

X-axis label.

annotate

A comma separated list or vector of custom stack annotations, e.g. '1,3,4,5,6,7' or c(1,3,4,5,6,7). Annotation list must be same length as sequences.

yaxis

Height of yaxis in units (default: maximum value with uninformative prior).

show.yaxis

Display entropy scale along y-axis? (default: TRUE).

ylabel

Y-axis label (default: depends on plot type and units).

show.ends

Label the ends of the sequence? (default: FALSE).

fineprint

The fine print text at the bottom right corner (default: blank).

ticmarks

Distance between ticmarks (default: 1.0).

errorbars

Display error bars? (default: FALSE).

reverse.stacks

Draw stacks with largest letters on top? (default: TRUE).

color.scheme

Specify a standard color scheme ('auto', 'base pairing', 'charge', 'chemistry', 'classic', 'hydrophobicity', 'monochrome').

stack.width

Width of a logo stack (default: 10.8).

aspect.ratio

Ratio of stack height to width (default: 5).

box

Draw boxes around symbols? (default: FALSE).

resolution

Bitmap resolution in dots per inch (DPI). Low resolution bitmaps with DPI

scale.width

Scale the visible stack width by the fraction of symbols in the column? i.e. columns with many gaps of unknowns are narrow (default: TRUE).

rotate.numbers

Rotate values of x-axis? (default: FALSE).

hide.tics

Hide tic marks? (default: FALSE).

Examples

Run this code

# Make a sequence logo using an external alignment file format
# In this example we'll use the EMBOSS alignment format or msf
# However, you can use any format supported by WebLogo e.g. fasta
fpath = system.file("extdata", "example_data.msf", package="RWebLogo")
weblogo(file.in=fpath)
# Now for an example using an alignment as an R character vector
aln <- c('CCAACCCAA', 'CCAACCCTA', 'AAAGCCTGA', 'TGAACCGGA')
# Simple WebLogo
weblogo(seqs=aln)
# Lets get rid of those ugly error bars and add some text!
weblogo(seqs=aln, errorbars=FALSE, title='Yay, No error bars!',
        fineprint='RWebLogo 1.0', label='1a')
# We can also change the format of the output like this
weblogo(seqs=aln, format='png', resolution=500)
# You can change the axis labels like this
weblogo(seqs=aln, xlabel='My x-axis', ylabel='Awesome bits')
# You get the idea! See ?weblogo for more awesome options!

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