You must validate each step (filtering, normalization) by clicking each button, even if you did not make any modification.

Otherwise you just need to click 'Launch all' button, then you can use others modules.

Input phyloseq object

Phyloseq preview


                      

STEP 1: Metadata table

STEP 2: Taxonomy rank and filtering options

STEP 3: Taxa filtering, preview abundances & representative sequences

Use filters to subset your dataset based on taxonomy.

Number of rows:

STEP 4: Abundance normalization

Final phyloseq object


                      

Phyloseq normalized object


                      

Color selection

Accepted formats for color assignation.

When the variable is a factor, modalities must be written in the first column of the Excel file and colors associated in hexadecimal code form in the second column.
When the variable is numeric, a palette must be chosen with the form package::palette written in the Excel file (only packages ggthemes and viridis are accepted).

Download xlsx file

                        
Download xlsx file

                      
Use phyloseq object without taxa merging step.

Settings:

Relative abundance:

Raw abundance:

Total sum per samples:


                    
Use phyloseq object without taxa merging step.

Settings:

Alpha indexes table

Alpha indexes by group

Boxplot

Use phyloseq object without taxa merging step.

Settings:

In this module, asv table is normalized by hellinger (Legendre & Gallagher 2001) method and environmental variables are centered and scaled.

Plot options

Ordination plot:

Screeplot

Reminder : This module launches Kruskal Wallis on factors for each taxa. Be aware that this is multiple testing, p.values are adjusted with FDR method. For numerical factors, samples with zero abundance are omitted

Settings:

Features:

Click on feature below to generate plot:

Boxplot:

Settings:

Differential analysis:

Run MGseq with same settings:

Run Metacoder wilcox test with fdr correction:

Merge results of differential analysis:

Plotting features:

Select conditions to highlight shared taxa

Settings:

Venn Diagram VennR:

Venn Diagram classic:

Venn table:

Click on rows to generate boxplot displaying raw abundance of the taxa.

Download Table

Boxplot Chart: (click on one taxa above)

Krona plot

Settings

Display settings

Settings:

Dendrogram


                        

Number of samples by cluster

Heatmap & Multilevel pattern analysis

Display heatmap of selected cluster

to

Determine taxa specific to each cluster


                      

sPLS-DA settings

Plot of individuals

Download plot

Plot of variables

Download plot

Biplot

Download plot

Features contribution

Download all sPLS-DA results