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The metaPR2 shiny application allowing access to the metaPR2 database is provided as a R package called metaPR2. This page provides instruction to install and use the package.

You can also:

Installation

Install from the GitHub web site using the devtools package

install.packages(devtools)
devtools::install_github("pr2database/metapr2-shiny")

Run the Shiny application

metapr2::metapr2App()

Stop the Shiny application

  • Close the browser window

OR

  • Hit the stop button at the top right of the bottom left window

In case Shiny application crashes

  • Hit the stop button at the top right of the bottom left window
  • Relaunch metapr2App()

Structure of the application

panel/subpanel content
Datasets Select and list datasets used. You can select also groups of datasets (e.g. arctic)
Treemap Create treemaps (square pie-chart) provinding the proportion of each taxon for the samples and datasets selected
Map Maps of read abundance. For a given taxonomic level you can visualize the proportions of the taxonomic levels below (e.g. species if you are at the genus level) or alternatively the main taxon at each station (e.g. the mainn species if you are the genus level). Size of circle is proportional to contribution of taxon to total eukaryotes.
Barplot Composition for specific variables (e.g. depth_level).
Diversity Diversity analysis using the R phyloseq package
- Alpha diversity Alpha diversity indices (e.g. Shannon, Simpson).
- Beta diversity Mutivariate analyses (e.g. NMDS).
Query Enter a sequence and search for metabarcode that are similar to your sequence using a BLAST like search. You can plot the ASVs matching your query.
Download Download data for selected samples/taxa as well as the whole dataset as a phyloseq file.
About Basic information on the metapr2 database.