Viewing the taxonomic data in Community Visualization
From the VAMPS Community Visualization page, select the datasets or custom datasets and the taxonomy you are interested in. For more information about selecting data, see Selecting Data for Comparison, and Simple or Custom Taxonomy in the Heatmap Comparison information. Choose whether you want to see NAs or not. Click the Taxonomy Table button.
The taxonomy for all the datasets will be shown in a table. Click the Hide Empty Taxa button to eliminate rows that have a count of 0. The table opens up with the absolute dataset counts.
The table will look slightly different if you select "Do not include NAs":
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Normalizing the data
The table opens up with the absolute dataset counts. Clicking Show By Frequency will show the data as a percentage in order to normalize the datasets against each other.
Clicking Show Normalized to Maximum will show the data at the same ratio as the percentage, but normalized to the count of the largest dataset.
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Viewing composition across datasets with piecharts
Click on one of the totals in the right hand column. This opens up a pie-chart with the composition of a specific taxonomy across datasets.
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Viewing unique sequences
Click on one of the pie-chart wedges to open up all the unique sequences in a dataset.
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Viewing reference sequences
Click on one of the sequences to see the reference sequence data for the sequence.
The read_ids can be downloaded into a file.
Scroll to the right in the reference data table. You will see a column containing the Ref SSU Id for the sequence.
Click the Ref SSU Id. This will take you to the reference page in the NCBI database.
