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 videosManual / Tutorial
The manual explains the behavior and options of each control element and analysis window.
Link to Manual / TutorialAlpha Diversity
Apply non-metrix multi dimensional scaling (NMDS) and other ordination methods, e.g. CA.
In this window OTU / ASV abundances are summarized by a taxonomic group. Different plot can be used to compare different samples.
To detect specialist and generalist different approaches are known. Here indicator species will be detected as specialist. Generalist will be detected by minimal abundance and minimal occurence.
We recommend to restrict the indicator species detection to the top expressed ASV/OTUs only.
Your selection includes the following number of features:
You can select the top x features based on order of your input table. Note: The order of your uploaded data is changed if sorting by mean before selection is active.
You can select most interesting feature by the mean of all samples. To view the distribution of the mean explore the plot below.
There are several concepts of (habitat) specialist or indicator species that slighly differ. Here we use the indicator value detection by Dufrene and Legendre (1997). The analysis requires two inputs: an abundance / count table and groups. The analysis output is two value for each feature (ASV/OTU/MAG): a P-value of statistical significance of enrichment in one of the groups and an indicator value showing the strength of indication for this group (value from 0 to 1), with higher values showing more specific enrichtment for the group. For more examples of how to find specific features or to interprete the results see the tutorial.
Download table
Generalist results:
Coming soon
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
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 !
Settings
Do you want to store your loaded and processed data? This enables automatic loading of the data on next app start.
ASV / OTU / MAG or feature table
Rarefaction
Relative abundance
Calculate relative abundance from raw data.
Apply cutoff for minimal abundance
You can apply a cutoff to remove low abundant ASV's or OTU's, e.g. rare biosphere.
Taxa table
Samples data table
Coming soon!
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.
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
Manage samples
Manage annotations
Data explorer
Control elements
This video explains the basic control elements and functions of the app.
How to create xxx
This video explains how to...