PAICE: Rapid pathway visualization Files

===============================================
PAICE 2.90 README
by Parsa Hosseini <Parsa.Hosseini@ars.usda.gov>
===============================================

Introduction
------------
As of PAICE 2.90, all functionality will be strictly via command-line;
providing easy integration into analysis pipelines.

PAICE (Pathway Analysis and Integrated Coloring of Experiments) is a
command-line Java tool for mapping KEGG-compatible accessions onto KEGG
pathways. Such mapping is performed given a tab-delimited text file 
with the accessions (column 1), and the experimental and control
values thereof (column 2 and 3, respectively).
The expression ratio (ratio between the experimental and control) will
ultimately determine the specific color displayed for that specific
accession: green if induced and red if suppressed. If an accession is
found multiple times with differing expression values, all occurrences
of that accession are colored yellow.
Shades of green and red are used for coloring accessions based on their
extent of expression.
The mean standard-deviation of all accessions' experimental vs control is
computed and used for detection-call analysis. This feature provides
additional insight into accessions whose levels of expression varies 
significantly greater in-comparison to the mean std. deviation.

PAICE is licensed under GPLv3, with source-code available at:
http://sourceforge.net/projects/paice/

Usage:
------
java -jar PAICE_v2_90.jar in_file <input file> out_dir <output folder> [options]

=== Optional flags ===

 -color_det_call_downreg <arg>	Hex color for suppressed detection-calls. [Default: #FF8800 (aka. orange)]
 -color_det_call_upreg <arg>	Hex color for induced detection-calls. [Default: #66EEAA (aka. cyan)]
 -color_heavily_downreg <arg>	Hex color for heavily suppressed accessions. [Default: #FF7F7F (aka. dark red)]
 -color_heavily_upreg <arg>	Hex-color for heavily induced accessions. [Default: #005804 (aka. dark green)]
 -color_lightly_downreg <arg>	Hex color for lightly suppressed accessions. [Default: #FF7F7F (aka. light red)]
 -color_lightly_upreg <arg>	Hex-color for lightly induced accessions. [Default: #7FFF86 (aka. light green)]
 -color_mod_downreg <arg>	Hex color for moderately suppressed accessions. [Default: #FF7F7F (aka. red)]
 -color_mod_upreg <arg>		Hex-color for moderately induced accessions. [Default: #00FF0D (aka. green)]
 -color_multiple_copies <arg>	Hex color for multiple accession-copies. [Default: #FFFF00 (aka. yellow)]
 -h,--help			Display this help message screen
 -std_dev <arg>                 A real-number representing mean std. deviation between all expt. and control
                                accessions; used in detection-call analysis.Higher the std. dev, the more accessions
                                will caught, and vice-versa. [Default: 'n/a' (aka. use default mean stdev between expt.
 -org_code <arg>                KEGG organism code. [Def: 'n/a' (accessions is EC)]
                                See http://www.genome.jp/kegg/catalog/org_list.html for org. codes.
=== Required flags ===
 -in_file <arg>			Input tab-delimited txt file (required). Must have 3x columns:
                                col 1 = KEGG-compatible accessions.
                                col 2 and 3 = experimental and control expression values, respectively. 
 -out_dir <arg>                 Output folder for saving pathways (required).
 

Contact:
--------
For any questions/comments, bugs or desired improvements, please
contact Parsa Hosseini <Parsa.Hosseini@ars.usda.gov>