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Chart visualization for metagenomics analysis tools AMPHORA2 and AmphoraNet. Related publication: http://dx.doi.org/10.1007/s00248-014-0502-6
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AmphoraVizu.pl
README
amphoravizu_sample_input.txt

README

AmphoraVizu, Chart visualization for metagenomics analysis tools AMPHORA2 and AmphoraNet

by Csaba Kerepesi, Balázs Szalkai, Vince Grolmusz

PIT Bioinformatics Group, http://pitgroup.org/

***Terms of Use:***

AmphoraVizu is free software: you can redistribute it and/or modify it under the terms of
the GNU General Public License as published by the Free Software Foundation, either
version 3 of the License, or any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY
WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.

***Help:***

- User Manual for AmphoraVizu: http://www.pitgroup.org/static/AmphoraVizu-Manual.pdf
- For any other inquiries send an Email to Csaba Kerepesi: kerepesics@gmail.com
- AmphoraVizu webserver: http://pitgroup.org/amphoravizu

***Quick start:***

1. Open Source AmphoraVizu is a program written in Perl programming language. Perl is downloadable from  https://www.perl.org/get.html
2. Use an AMPHORA2 or AmphoraNet output file as input file (sample files are available here: http://www.pitgroup.org/static/amphora2_results/ ) 
3. A typical command: 
perl AmphoraVizu.pl -input example_output.txt -min_confidence 0.1 -lowest_rank 2 -min_average 0.02 -chart_type column > out.html
4. Finally open the out.html file in a web browser. 

***Options:***

-input: input file (AMPHORA2 output file), default: /dev/stdin
-min_confidence: minimum confidence, default: 0.1
-lowest_rank: lowest rank (1=Superkingdom, 7=Species), default: 2
-min_average: minimum average to display, default: 0.02
-chart_title: chart title (with optional HTML tags), to override default title
-chart_type: "column": Column Chart output (default), "pie": Pie chart output with averages
-chart_width: width of chart area, all CSS values are valid (default: 100%)
-chart_height: height of chart area (default: 100%)
-chart_compact: if 1, margins are decreased as much as possible (default: 0)
-html_inline: if 1, tags like <html>, <head> and <body> are omitted (default: 0)     
-miniview: 1: miniview on, 0: miniview off (default: 0)      
-sort: "avg": sorted by averages (default), "abc" sorted by alphabet
-quantify: "prop": shows the proportions of marker genes (default), "amounts": shows the exact amounts of marker genes
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