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Open sample information

Welcome to the biodiversity explorer app

This interactive app offers you a simple way of analyzing and playing with the microbial commuminty data.

You can explore raw data, merge replicate samples, perform state-of-the-art analysis and find interactive visualizations.

To learn how the app works and what you can do watch a short intro video, check the online manual / tutorial or simply explore on your own.


Demo videos

The intro video will show you the most important functions and basic bahavior:

Link to videos

Manual / Tutorial

The manual explains the behavior and options of each control element and analysis window.

Link to Manual / Tutorial

Venn diagram showing the overlap of OTUs for selected samples. Select 2 to 5 samples to compare


Save plot

PCA plot: It show all samples or only specific samples (when 2 or more selected)

Explained variance of PCs

Absolute of the Loadings

Apply non-metrix multi dimensional scaling (NMDS) and other ordination methods, e.g. CA.


Hierarchical clustering of selected samples. Please select three or more samples.

Experimental: Heatmap of samples including clustering. ! Currently no change in clustering method available for this plot !




Bubble plot of function annotation classes and samples.

Save plot






Correlation of groups

Download

In this window OTU / ASV abundances are summarized by a taxonomic group. Different plot can be used to compare different samples.


Correlation of groups

Download

Select a sample to use for the pie plot. By clicking a pie of the plot pie another pie with details for the selected pie is shown below.


Heat map of all non-zero rows for the selected samples


Bubble plot of selected samples and taxonomic groups.

Save plot




Data table showing the abundance data with applied cutoff (values below cutoff are set to 0)

Data table showing the functional annotation



Table of merged sample. Select row in the table to edit, or create new.

Order samples by drag and drop. Missing samples will be added on saving in there default order.



Table of annotations. Select row in the table to edit, or create new.

Manual and tutorial for the Biodiversity App

This interactive app offers you a simple way of analyzing and playing with the microbial commuminty data.

Using OTU or ASV count tables you can

  • Explore the data
  • Merge replicates
  • Perform state-of-the-art analysis and find interactive visualizations

Control elements

Side bar

The side bar is divided into two different boxes: The data selection and the plot setting box. Change of input to the side bar will effect all windows.

Data selection

  • Sample selection: The data selection offers to select the samples of interest that should be analyzed or visualized. Samples have a long and a short name. In the graphs only the short name is shown.
  • Cutoff (minimal abundance): This parameter controls the abundance cutoff of OTU's (or ASV's) to filter. The default setting of 0.001 will remove OTU's with less than 0.1% of total abundance.

Plot settings

The plot setting allow to change different parameters of the visualization, as they are key to explore the data:

  • Color set: The colors for different samples (if applicable). The colors can be set in the “Manage samples” window.
  • Sample order: The order might be important for arranging similiar sample next to each other. The order can be set in “Manage samples” window.
  • Interactive plot: Most plots are interactive, generated with plotly. They allow hover to show exact value or name, allow to select samples are groups, allow zooming and more. You can also produce snapshots of the interactive plots via the camara icon that appear while hover of the top right corner of a plot. However, sometime a static plot might be better (e.g. to show the full legend). You can change to non-interactive plots generate by ggplot. You can save these plots by clicking the “Save” button that should appear.
  • Horizontal bar plot: The app has a set of visualizations using bar plots. By default the bars are vertically oriented. With this checkbox you can change to horizontally oriented.
  • More plot settings: This box offers a set of detailed parameters to change the plots. Not all parameters are working with all plots. If labels are to small try to change the label size or X/Y-axis label size. It the axis labels are not fully visable try to change the left or bottom margin.

Menu structure

The menu on the top of the page allow to switch between different windows with different functionality:

  • Home: Start page
  • “Sample similarity” and “Functional annotation”: offer to analyze your data.
  • Data explorer: offers inspect the used data to verify that the data was correctly loaded.
  • Manage and customize: – Manage samples: – Manage Annotation:
  • Help and tutorial:
  • User: Login to make permanent changes.

Analysis and Visualisations

PCA

NMDS

VennDiagram

Mana

Control elements

This video explains the basic control elements and functions of the app.

How to create xxx

This video explains how to...