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
Download RAW tables
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).
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:
Aggregate table:
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 TableBoxplot 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
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