Alpha diversity

For quick access

Step2. Choose the metadata of all your samples with the sample name as the first column.

REMEMBER to declaim your column for grouping in the parameter if you are not using 'phenotype'.

Step3. Click Submit and wait.

The description of every input you can find by holding on the (?) symbol after the input names.

Introduction

Module Alpha diversity calculates the alpha diversity of samples using the Shannon index based on the profiling from different taxonomy levels.

You can find the demo output and visualization here.

The description of every input you can find by holding on the (?) symbol after the input names. A details description also listed:

Inputs

Input: group_info*

Group information (TSV file). The group information of samples to participate in the analysis, only exactly two groups are allowed now. If you want to use the personal dataset from the build-in database, you should also set the group of those samples in this input.

header

ID	Group
sample1	case

rows
sample ID and the group information for the corresponding sample.

Input: user_abd (should have if no second_i select)

Profiling table (TSV file). The file contains the relative abundance of samples.

header/column names

Samples ID separated with tab.

row names

Taxonomy names in mpa format. (MetaPhlAn3 default output is acceptable)

For each species, the input should have a complete record from kingdom to species:

k__Bacteria
k__Bacteria|p__Actinobacteria
k__Bacteria|p__Actinobacteria|c__Actinobacteria
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Actinomycetales
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Actinomycetales|f__Actinomycetaceae
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces_odontolyticus

Input: second_i (should have if no user_abd upload)

Select the dataset you constructed from the build-in database you want to use in the analysis.

Outputs

Output: Alpha diversity of samples (TSV files)

Outputs names: main result__Alpha_diversity.tsv

These files contain a table of samples with alpha diversity from different taxonomy levels.

Example:

	sample
k	0.105196
p	2.134787
c	2.459631
o	2.50097
f	3.349231
g	3.768799
s	4.243575
t	4.012784

The row names are the taxonomy levels in short: k for Kingdom, p for phylum, c for class, o for order, f for family, g for genus, s for species, and t for strain.

Output: P-value of comparison alpha diversity between groups in different taxonomy levels (TSV files)

Outputs names: p-value__Alpha_diversity_pvalue.tsv

These files contain a table of p-values in different taxonomy level:

Example:

	p-value
k	0.0855812266232
p	0.367853563556
c	0.664404471969
o	0.28019192343
f	0.428741461583
g	0.334140479765
s	0.0597413184597
t	0.0674838617367

The row names are the taxonomy levels in short: k for Kingdom, p for phylum, c for class, o for order, f for family, g for genus, s for species and t for strain.

Manual version=1.0, written by Dr. JIANG Yiqi on 2022-04-19.

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