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How to Use VAMPS



  • Introduction

  • Community Visualization - Heatmap Comparison

  • Community Visualization - Taxonomy Tables

  • Exporting Taxonomic Counts

  • Exporting Clustering and Diversity Data

  • Exporting Fasta Sequences

  • Heatmap Comparison

    Selecting Data for Comparison

    From the VAMPS Community Visualization page, click Select and Analyze.

    You will see three panels, one for selecting datasets, one for selecting custom datasets, and one for selecting taxonomy. Check the boxes for the datasets you want to analyze, including custom datasets. Select Simple Taxonomy, and check the domains you are interested in, along with the taxonomic level desired.

    Selecting Projects and Datasets

    Start by selecting a project name in the left-hand column. When clicking on a project name you will see all the datasets that are part of that project. See definition of projects and datasets. The projects are listed by project name and project title. In the example below, the project name is "DAR_HCT_Bv6" and the project title is "Human ciproflaxin". Hovering the mouse pointer over the project will show a more detailed description of the project. The project naming convention includes a suffix, Bv6, Av6, etc., indicating whether the domain of the project is archaea, bacteria, or eukarya, and which hypervariable region, v3, v6, or v9, is used.

    In the middle column you can select any Custom Datasets you have defined on the Customize Datasets page. Clicking on the custom dataset name itself will show the components of that dataset.



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    Selecting Simple or Custom Taxonomy

    In the taxonomy selection panel, you can select Simple or Custom Taxonomy. With Custom Taxonomy you can choose more specific data, for example one particular phylum. With Simple Taxonomy you will get all taxonomies in the selected domain down to the chosen taxonomic level.

    Another option available is Clade or Individual radio button. Having Clade selected will select all open levels of the clade you are clicking. This enables you to select multiple taxonomies at once. Selecting Individual lets you click and select single check boxes.

    To open the taxonomy levels, double-click on on a taxonomy name. Each time you double-click, the tree opens up one level, for example double-clicking once opens the phyla, double-clicking again open the classes. Clicking in a checkbox toggles check marks off and on in the lowest level that is open below the one you are clicking.

    In the example below, clicking in the phylum Acidobacteria selects all families available in the phylum where available. If the family is not available, the closest available level above will be selected.

    Once you have multiple taxonomies selected, you can go back and deselect specific taxa that you want to exclude.



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    Viewing the heatmap

    Click Community Comparison Heatmap.

    The heatmap will show all the datasets compared to each other. A darker blue color means the samples are of a similar taxonomy. The colors grade from blue, through white, to red for dissimilar taxonomy.



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    Sorting the heatmap

    You can sort the rows according to similarity by clicking in the dataset column on the left and dragging the entire row to a different spot.



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    Comparing two datasets with piecharts

    To compare two individual datasets with each other, you can click in the corresponding square on the heatmap. You will see two piecharts, one for each of the two datasets. The piechart shows the taxonomic composition for each of the datasets. In the example below, dataset FP4 is being compared with BB7.

    Options allow you to sort the data in order of abundance:



    or in alphabetical order:



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    Other formats: Distance, Bray-Curtis/Jaccard, Jaccard/Yue-Clayton, and Yue-Clayton/Bray-Curtis

    If you go back to the original heatmap page, you can also view the data in other formats.

    As distance:



    Bray-Curtis/Jaccard:



    Jaccard/Yue-Clayton:



    Yue-Clayton/Bray-Curtis:



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    Trees

    If you go back to the original heatmap page, you can also choose to view the data in tree format.

    UPGMA format:



    Neighbor Joining format:



    Fitch format:



    Kitsch format:



    You have the option to view the same trees in ascii format:



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    Bargraphs

    Going back to the original heatmap page, you can also view the composition of data as bargraphs.







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