proScatter 0.0.2

Description:

proScatter 0.0.2

For visualizing pLink data from one or more experiments
by Katelyn McGary Shipper, Justin Jee, and Ilya Shamovsky
Dependencies
proScatter uses python,
numpy,
bokeh, and
pandas
Basic Use
To download, either download all 3 .py files into the same directory, or
download the zipped folder (see button on the bottom right)
The inputs to proScatter include:

A fasta file including the amino acid sequences of all the proteins
under consideration.
A list of amino acids of interest (ex: K or CM)
pLink output in .html format

The outputs include:

A summary file (.txt) containing the list of all links and their
frequencies
A scatter plot

Example
./proScatter.py examples/test.fasta examples/IdProTable_combine.html


Features
proScatter enables multiple features, for example:
python proScatter.py test.fasta K test.html --scale --zoom=Prot1-Prot2 --evalue=0.001
Details are given below:
–scale
Scales both plot and output so that only the amino acids of interest are
considered. Axes are in units of amino acids of interest (ex: 1st
lysine, 2nd lysine, etc)
–zoom=Prot1-Prot2
Zooms in on only one subplot (Prot1 vs Prot2). As an added feature,
clicking on any point in the scatter plot will print the coordinates of
that point in the console.
–evalue=#
Considers only links with a score below a certain number #. Scores are
expected to be in the 5th column
usage: proScatter.py [-h] [-a AMINOACIDS] [-z ZOOM] [-s] [-e EVALUE] [-u]
[-o OUTPUT] [-v]
fasta_file plink

positional arguments:
fasta_file fasta file with protein sequences
plink pLink output .html file

optional arguments:
-h, --help show this help message and exit
-a AMINOACIDS, --aminoacids AMINOACIDS
cross-linkable aminoacids. Defaults to Lysine (K).
-z ZOOM, --zoom ZOOM Prot1-Prot2 only display subplot for proteins Prot1 vs
Prot2
-s, --scale scale both plot and outputs so that only amino acids
of interest are considered
-e EVALUE, --evalue EVALUE
e-value cutoff
-u, --unjoin unjoin plot axes
-o OUTPUT, --output OUTPUT
output file (HTML) name
-v, --verbose increase output verbosity