10. Taxonomical Bar Chart - raytonghk/genepiper GitHub Wiki

Taxonomical Bar Chart module provides a method to visualise the abundance of taxa in all samples at a specified taxonomic rank. It is commonly done for comparison of community composition at a higher taxonomic rank (e.g. Phylum).

Load Data and Subsample

Analysis starts from loading data in the Load Data panel. User can select the project and data label to load the saved data. After loading data, subsampling can be done in the Filter panel if needed.

Parameters

Taxonomic Rank For Agglomeration: select the taxonomic rank to agglomerate the counts of reads in samples.

Abundance Type: choose between Raw Count (original read counts), Rarefied Count (Rarefying sample read counts to the lowest count amongst samples) and Relative Abundance (counts are divided by the sum of counts in each sample).

Prevalence (%): filter the taxa based on their prevalence in percentage (fraction of total number of samples in which a taxon is observed)

Display: options to show all the taxa in the plot or filter by the abundance and show only the top n taxa (n is defined by user).

Result

This module produces stacked bar chart showing the composition of microbiota at a specified taxonomic rank. The plot can be downloaded by clicking the Download button.

Graphic Parameters

The Graphic Parameters panel provides options in the Title, Axis and Legend tabs to customise the plot.

The Group Column option in Group tab allows grouping of samples by a variable in the sample data table. With group assigned, the label of each sample on the x-axis will be coloured and arranged in an order according to the grouping.