weblogo: Plot a sequence logo
In RWebLogo: plotting custom sequence logos
Description
Usage
Arguments
Examples
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
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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<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).
rotate.numbers
Rotate values of x-axis? (default:
FALSE).
hide.tics
Hide tic marks? (default: FALSE).
Examples
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# 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!
Example output
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Error in find_python_cmd(minimum_version = minimum_version, maximum_version = maximum_version, :
Couldn't find a sufficient Python binary. If you haven't installed the Python dependency yet please do so. If you have but it isn't on the system path (as is default on Windows) please add it to path or set options('python_cmd'='/path/to/binary') or set the PYTHON, PYTHON2, or PYTHON3 environmental variables. Python must be at least version 2.6 Python must have access to the modules: numpy
Please install and add Python (>=2.6) to your path
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Error in find_python_cmd(minimum_version = minimum_version, maximum_version = maximum_version, :
Couldn't find a sufficient Python binary. If you haven't installed the Python dependency yet please do so. If you have but it isn't on the system path (as is default on Windows) please add it to path or set options('python_cmd'='/path/to/binary') or set the PYTHON, PYTHON2, or PYTHON3 environmental variables. Python must be at least version 2.6 Python must have access to the modules: numpy
Please install and add Python (>=2.6) to your path
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Error in find_python_cmd(minimum_version = minimum_version, maximum_version = maximum_version, :
Couldn't find a sufficient Python binary. If you haven't installed the Python dependency yet please do so. If you have but it isn't on the system path (as is default on Windows) please add it to path or set options('python_cmd'='/path/to/binary') or set the PYTHON, PYTHON2, or PYTHON3 environmental variables. Python must be at least version 2.6 Python must have access to the modules: numpy
Please install and add Python (>=2.6) to your path
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Error in find_python_cmd(minimum_version = minimum_version, maximum_version = maximum_version, :
Couldn't find a sufficient Python binary. If you haven't installed the Python dependency yet please do so. If you have but it isn't on the system path (as is default on Windows) please add it to path or set options('python_cmd'='/path/to/binary') or set the PYTHON, PYTHON2, or PYTHON3 environmental variables. Python must be at least version 2.6 Python must have access to the modules: numpy
Please install and add Python (>=2.6) to your path
[1] 1
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Error in find_python_cmd(minimum_version = minimum_version, maximum_version = maximum_version, :
Couldn't find a sufficient Python binary. If you haven't installed the Python dependency yet please do so. If you have but it isn't on the system path (as is default on Windows) please add it to path or set options('python_cmd'='/path/to/binary') or set the PYTHON, PYTHON2, or PYTHON3 environmental variables. Python must be at least version 2.6 Python must have access to the modules: numpy
Please install and add Python (>=2.6) to your path
[1] 1
RWebLogo documentation built on May 2, 2019, 2:26 a.m.
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Description Usage Arguments Examples
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
1 2 3 4 5 6 7 8 9 10 | 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 |
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 |
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 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). |
rotate.numbers |
Rotate values of x-axis? (default: FALSE). |
hide.tics |
Hide tic marks? (default: FALSE). |
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | # 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!
|
Example output
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Error in find_python_cmd(minimum_version = minimum_version, maximum_version = maximum_version, :
Couldn't find a sufficient Python binary. If you haven't installed the Python dependency yet please do so. If you have but it isn't on the system path (as is default on Windows) please add it to path or set options('python_cmd'='/path/to/binary') or set the PYTHON, PYTHON2, or PYTHON3 environmental variables. Python must be at least version 2.6 Python must have access to the modules: numpy
Please install and add Python (>=2.6) to your path
[1] 1
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Error in find_python_cmd(minimum_version = minimum_version, maximum_version = maximum_version, :
Couldn't find a sufficient Python binary. If you haven't installed the Python dependency yet please do so. If you have but it isn't on the system path (as is default on Windows) please add it to path or set options('python_cmd'='/path/to/binary') or set the PYTHON, PYTHON2, or PYTHON3 environmental variables. Python must be at least version 2.6 Python must have access to the modules: numpy
Please install and add Python (>=2.6) to your path
[1] 1
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sh: 1: cannot create /dev/null: Permission denied
Error in find_python_cmd(minimum_version = minimum_version, maximum_version = maximum_version, :
Couldn't find a sufficient Python binary. If you haven't installed the Python dependency yet please do so. If you have but it isn't on the system path (as is default on Windows) please add it to path or set options('python_cmd'='/path/to/binary') or set the PYTHON, PYTHON2, or PYTHON3 environmental variables. Python must be at least version 2.6 Python must have access to the modules: numpy
Please install and add Python (>=2.6) to your path
[1] 1
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sh: 1: cannot create /dev/null: Permission denied
Error in find_python_cmd(minimum_version = minimum_version, maximum_version = maximum_version, :
Couldn't find a sufficient Python binary. If you haven't installed the Python dependency yet please do so. If you have but it isn't on the system path (as is default on Windows) please add it to path or set options('python_cmd'='/path/to/binary') or set the PYTHON, PYTHON2, or PYTHON3 environmental variables. Python must be at least version 2.6 Python must have access to the modules: numpy
Please install and add Python (>=2.6) to your path
[1] 1
sh: 1: cannot create /dev/null: Permission denied
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sh: 1: cannot create /dev/null: Permission denied
sh: 1: cannot create /dev/null: Permission denied
Error in find_python_cmd(minimum_version = minimum_version, maximum_version = maximum_version, :
Couldn't find a sufficient Python binary. If you haven't installed the Python dependency yet please do so. If you have but it isn't on the system path (as is default on Windows) please add it to path or set options('python_cmd'='/path/to/binary') or set the PYTHON, PYTHON2, or PYTHON3 environmental variables. Python must be at least version 2.6 Python must have access to the modules: numpy
Please install and add Python (>=2.6) to your path
[1] 1
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