AmphoraVizu

Chart visualization for the metagenomic and genomic analysis tools AMPHORA2 and AmphoraNet

AmphoraVizu can visualize outputs generated by the metagenomic and genomic analysis tool AMPHORA2 or its webserver implementation AmphoraNet.

AMPHORA2/AmphoraNet output:	[?]Select an AMPHORA2/AmphoraNet output file.
Lowest taxonomic rank:	[?]Select the lowest taxonomic rank you are interested in.
Chart type: Show advanced options	[?]The Column Chart shows the distribution of phylotypes for each marker gene. The Pie Chart shows the consensus distribution (averages of the distributions for each phylotype).

Using AmphoraVizu step by step

Upload an AMPHORA2 or AmphoraNet output file.
Sample input file (HMP - buccal mucosa metagenome analysed by AmphoraNet). More input files
Select the lowest taxonomic rank which you are interested in.
You can use the advanced options choose the display mode, the lower bound for the confidence, the average share and the title. There is a link to display these options.
Click the "Visualize!" button. You will see a chart immediately (if it is not too wide to display in miniview). Then click "Magnify" for the magnified chart. You can download a HTML file with the chart as well. Sample outputs: Column Chart, Pie Chart.

More details and help

For or more details please check these links and article:

If you have any questions or ideas related to AmphoraVizu, please feel free to contact us (kerepesics@gmail.com, Csaba Kerepesi) or visit the AmphoraVizu forum topic on Biostars.

Open-source AmphoraVizu

The open-source version of AmphoraVizu is downloadable from here: AmphoraVizu.pl. Also available on GitHub.

Terms of use

You can use this service only if you accept the following terms: We do not guarantee anything about this service: We do not state anything about the usability of this service, and we do not state that the results that we may return can be used for any purpose. We cannot guarantee that this service will be available in the future, and we cannot guarantee that your query would generate any output at all.

Privacy: We will not give out your data to anyone.

How to cite: If you publish anything using the output of AmphoraVizu webserver, you are asked to cite the following publication, and you are also suggested to refer to the web address of our webservice:

Csaba Kerepesi, Balázs Szalkai, Vince Grolmusz. Visual Analysis of the Quantitative Composition of Metagenomic Communities: the AmphoraVizu Webserver. Microbial Ecology, April 2015, Volume 69, Issue 3, pp 695-697, http://dx.doi.org/10.1007/s00248-014-0502-6.

Display mode:	[?]Proportion: for each marker gene, the ratio of hits is displayed which correspond to the specific phlotype. That is, the total hit count is normalized to 1 for each marker gene. Amount: the exact number of hits is displayed for each marker gene and phylotype.	Proportion Amount
Minimum confidence:	[?]The minimum confidence of hits to consider (0..1).
Minimum average to show:	[?]Only those phylotypes will be displayed whose average share is at least the given value (0..1).
Title of magnified chart:	[?]The following parameter references can be used in the title: `$chart_type, $filename, $lowest_rank, $min_average, $min_confidence`.