1 Intro
This report provides some basic description and visualization of the MetaLab function results.
Users can use this to quickly check the functional profile of the input data set.
2 Sample overview
| Protein groups annotation | Number (percentage) |
|---|---|
| Protein groups in your sample | 19411 |
| Protein groups with COG annotation: | 19411 ( 100% ) |
| Unique COG accessions annotated: | 1876 |
| Protein groups with NOG annotation: | 19411 ( 100% ) |
| Unique NOG accessions annotated: | 5186 |
| Protein groups with KEGG ko annotation: | 19411 ( 100% ) |
| Protein groups with GO annotation: | 19411 ( 100% ) |
| Protein groups with EC annotation: | 19411 ( 100% ) |
| Protein groups with CAZy annotation: | 19411 ( 100% ) |
Grouping 1: group1; group2; group7
Grouping 2: control; treamtment
3 Overview with voronoi plots
About this plot
- COG: Clusters of Orthologous Genes
- More about COG
- The eggNOG database is a database of biological information hosted by the EMBL. It is based on the original idea of COGs (clusters of orthologous groups) and expands that idea to non-supervised orthologous groups constructed from numerous organisms.[4] The database was created in 2007[5] and updated to version 4.5 in 2015.[1] eggNOG stands for evolutionary genealogy of genes: Non-supervised Orthologous Groups. More about NOG
- Areas is based on the total intensity across samples
- Graph is by voronoiTreemap
3.1 COG categories
3.2 eggNOG categories
4 Overview with composition bar plots
About this plot
4.1 COG
4.1.1 Raw
4.1.2 Normalized
4.2 NOG
4.2.1 Raw
4.2.2 Normalized
5 Clustering of COGs
- There are 1877 features.
- With 623 100% presence across experiments (Q100).
5.1 Interactive heatmap
About this plot
- If there are more than 100 Q100 features, only the top100 will be used for this interactive plot
- if there are no Q100 features, top100 will be used with +1
- data is transformed by log10
- Scale on feature wise to be mean as 0, and sd as 1
- plot was generated by heatmaply::heatmaply
5.2 Static Heatmap
About this plot
- All Q100 features are used for this static plot, if there are no Q100, Q50 will be used, by +1
- transform by log10
- Scale on feature wise to be mean as 0, and sd as 1
- Plot was generated by complexheatmap::pheatmap
5.3 Hierarchical cluster
About this plot
- All intensity values +1
- transform by log10
- Scale on feature wise to be mean as 0, and sd as 1
- Calculate the distance between features, using euclidean method
- Do Hierarchical cluster analysis, with method = “complete”
5.4 PCA Contribution
- Screeplot
- Contribution
5.5 PCA without Grouping
5.5.1 2D plot
5.5.2 3D Scatterplot
5.6 PCA with Grouping: group1; group2; group7
5.6.1 2D plot
5.6.2 3D plot
5.6.3 All PC pairs
5.7 PCA with Grouping: control; treamtment
5.7.1 2D plot
5.7.2 3D plot
5.7.3 All PC pairs
6 Clustering of NOGs
- There are 5187 features.
- With 903 100% presence across experiments (Q100).
6.1 Interactive heatmap
About this plot
- If there are more than 100 Q100 features, only the top100 will be used for this interactive plot
- if there are no Q100 features, top100 will be used with +1
- data is transformed by log10
- Scale on feature wise to be mean as 0, and sd as 1
- plot was generated by heatmaply::heatmaply
6.2 Static Heatmap
About this plot
- All Q100 features are used for this static plot, if there are no Q100, Q50 will be used, by +1
- transform by log10
- Scale on feature wise to be mean as 0, and sd as 1
- Plot was generated by complexheatmap::pheatmap
6.3 Hierarchical cluster
About this plot
- All intensity values +1
- transform by log10
- Scale on feature wise to be mean as 0, and sd as 1
- Calculate the distance between features, using euclidean method
- Do Hierarchical cluster analysis, with method = “complete”
6.4 PCA Contribution
- Screeplot
- Contribution
6.5 PCA without Grouping
6.5.1 2D plot
6.5.2 3D Scatterplot
6.6 Grouping: group1; group2; group7
6.6.1 2D plot
6.6.2 3D plot
6.6.3 All PC pairs
6.7 Grouping: control; treamtment
6.7.1 2D plot
6.7.2 3D plot
6.7.3 All PC pairs
7 Binary comparsion
7.1 COGs
7.1.1 meta1
7.1.2 meta2
7.2 NOGs
7.2.1 meta1
7.2.2 meta2
