weblogo: Plot a sequence logo
In omarwagih/RWebLogo: plotting custom sequence logos

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

weblogo(seqs, file.in, open = TRUE, verbose = TRUE, plot = F,
  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)

`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).
`plot`	Plot the resulting logo as an R plot? Note: in order for this to work, the format option must be set to `jpeg` (default: FALSE).
`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<300 are antialiased (default: 300 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).

# 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')
# You can change the axis labels like this
weblogo(seqs=aln, xlabel='My x-axis', ylabel='Awesome bits')
# Lets try plot a web logo to the R graphics device
weblogo(seqs=aln, plot=TRUE, open=FALSE, format='jpeg', resolution=600)
# You get the idea! See ?weblogo for more awesome options!
# See ?plotlogo for more information on plotting jpeg sequence logos to the R graphics device!