1 Intro
This report provides some basic description and visualization of the MetaLab taxonomy results. The report is based on the taxa.refine.txt, which is a node based hierarchical like data Users can use this to quickly check the taxonomic profile of the dataset at each taxonomic level. For more taxon tree view, please go to MetaMap report section
2 Sample overview
Number of samples in your dataset: 13
Number of species identified: 585
Number of genera identified: 411
Number of families identified: 121
Number of orders identified: 55
Number of classes identified: 25
Number of phyla identified: 20
Grouping 1: group1; group2; group7
Grouping 2: control; treamtment
3 Overall pattern
About this plot
- Intensity is based on the total intensity across samples
- Graph is plotted by suburstR::sund2b
- Tree is plotted by networkD3::diagonalNetwork
- Node without labeling is not present
3.1 sunburst
3.2 Tree
4 Species level Sample Clustering/Similarity
About this clustering Diversity
- sample clustering based on the species-level composition
- Distance measure used is “euclidean” (dist(x,method = “euclidean”))
- clustering method: hclust(distance, method= “ward.D”)
- Clustering analysis will be performed when there are more than 2 samples
5 Richness
What is richness
- Identification count on different levels
- [ref
- More detailed References
- R package used for calculation: tabula
5.1 meta1
5.2 meta2
5.3 Result table for download
6 Heterogeneity and Evenness
Alpha Diversity
- Heterogeneity and Evenness belongs to the concept of alpha diversity
- We only show Shannon-Wiener index in this plot
- the diversity was calculated by vegan::diversity(x,index = “shannon”)
- more details about what is types of diversity and the way of calculation
- References
- R package used: vegan and tabula
6.1 meta1
6.2 meta2
6.3 Result table for download
7 Beta diversity
Beta Diversity
- here we only show Bray Curtis dissimilarity as one of the beta diversity
- The data is based on species level
- The caclculation is done by vegan::vegdist(t(count_species),method=“bray”)
- Visualization by PCoA
- more details about what is types of diversity and the way of calculation
- References: https://en.wikipedia.org/wiki/Bray%E2%80%93Curtis_dissimilarity
- R package used: vegan and tabula