In compbiomed/animalcules: Interactive microbiome analysis toolkit

knitr::opts_chunk$set(echo = TRUE)

Relative Abundance Stacked Bar Plot

The stacked bar plots are used to visualize the relative abundance of microbes at a given taxonomical level in each sample represented as a single bar.

Instructions:

Select taxonomy level in the menu (default is genus)
(Optional) Add a color bar for one of more sample conditions
(Optional) Group samples and aggregate abundances by a condition
(Optional) Sort samples by conditions or the presence of specific organisms
(Optional) Select "Advanced Options" to view:
- (Optional) Isolate or discard samples
- (Optional) Order organisms
- (Optional) Hide or show legend (default is to show legend)
- (Optional) Adjust plot height
- (Optional) Adjust plot width
Click the button "Plot"

Relative Abundance Heatmap

The heatmap represents a sample by organisms matrix that can be visualized at different taxonomic levels.

Instructions:

Select taxonomy level in the menu (default is genus)
(Optional) Add a color bar for one of more sample conditions
(Optional) Sort samples by conditions or the presence of specific organisms
(Optional) Select "Advanced Options"
- (Optional) Isolate organisms or samples
- (Optional) Discard samples
- (Optional) Use raw counts or log(CPM) (default is log(CPM))
- (Optional) Adjust plot height
- (Optional) Adjust plot width
Click the button "Plot"

Relative Abundance Boxplot

The boxplot visualization allows users to compare the abundance of one or more organisms at multiple taxonomical levels between categorical attributes.

Instructions:

Select one or more taxonomy levels in the menu (default is genus)
For each taxonomy level select one or more organisms to compare
(Optional) Separate plots when viewing multiple organisms on the same taxonomy level
Select a condition to compare organisms across
Select a datatype to use
(Optional) Select "Advanced Options"
- (Optional) Select a custom plot height
- (Optional) Select a custom plot width
Click the button "Plot"