Biome-Shiny v1.0

Data Upload

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Data Type

Biom file

Sample dataset

Type of biom file:

.biom file with sample variables

.biom file with .csv metadata file

.biom file without .csv metadata file

Dataset:

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OTU Table: Samples are columns

.csv metadata file (sample variables):

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Taxonomy parsing function

Choose a sample dataset:

Rarefaction
Top taxa
Subset taxa
Remove samples
Data Filtering and Transformation

Rarefy dataset

Seed

Sample with replace

Remove non-top taxa

Number of top taxa:

Subset taxa by taxonomy rank

Taxa rank:

Taxa:

Remove unchecked samples

Samples:

Activate changes

Set as active dataset

Phyloseq Summary

Sample variables:

Settings

Sample variable:

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Group samples by metadata variable (facet_wrap)

Metadata:

Taxonomy

Taxonomic rank:

Plot Settings
Plot

Variables

Samples:

Point color:

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Sort samples by metadata variable

Sample sorting metadata:

Diversity measure:

Observed

Chao1

ACE

Shannon

Simpson

InvSimpson

Fisher

Abundance (Counts)
Abundance (Relative)

Ordination Plot
Taxa Plot

Variables
Plot

Variables

Metadata:

Ordination method:

Distance:

Aesthetic options:

Dataset: Transform data with Hellinger method

Point size:

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Variables
Plot

Variables

Taxonomy rank:

Ordination method:

Distance:

Aesthetic options:

Point size:

Enable facet_wrap

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Variables
Data Tables

Variables

Dissimilarity index:

Sample variable:

Number of permutations:

P-Value table

Homogeniety table

Variables
Plot

Variables

Dissimilarity index:

Sample variable:

Number of permutations:

Variables
Plot

Variables

Distance method:

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Sample variable to cluster data samples:

Sample variable to set different point shapes:

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