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
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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
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
ggplot2 or plotly
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 with same settings:
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
New Heatmap module.
Ecology organized heatmap. Row an columns are organized using ordination methods (NMDS, PCA) and computed on ecological distances (bray, unifrac, jaccard).
Please cite:
doi:10.1186/1471-2105-11-45
Settings
Plot size
Settings
The heatmap is generated with preformated (filtered, agglomerated to rank...) data and normalized with method chosen in the 'Input data' module (VST is recommended).
Settings:
Leaf label
Branch color based on cluster or metadata
Dendrogram
Number of samples by cluster
Heatmap & Multilevel pattern analysis
Display heatmap of selected cluster
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