Visualisation of the data

1 Krona

Krona is an interactive visualisation tool for exploring metagenomic species abundance.

1.1 Running Krona

We can use the Kraken2 report files to create Krona plots. The following command imports taxonomy information from the Kraken2 report files and generates an interactive HTML file.

ktImportTaxonomy -o kraken2.krona.html *.kreport2
  • -o specifies the output HTML file
  • *.kreport2 matches all Kraken2 report files in the current directory
    • The * wildcard matches any characters, meaning this will include K1.kreport2, K2.kreport2, and W1.kreport2
Note

You may see a warning indicating that some taxonomy IDs were not found. This can be ignored for this practical. In future analyses, this should be resolved by running Krona’s taxonomy update command:

ktImportTaxonomy.sh

1.2 Visualising Krona plots

The Krona plot can be viewed in a web browser.

firefox kraken2.krona.html &

The Krona output is an interactive, multi-layered pie chart. Key features include:

  • To switch between samples, click the sample name in the top left
  • To zoom into a lower taxonomic level, double-click a taxonomy name on the chart
  • To zoom out, click the taxonomy name in the centre of the chart
  • To view percentage statistics, click on a taxonomy name

2 Pavian (alternative to Krona)

Pavian is an interactive Shiny-based application for exploring metagenomic taxonomic classification results, including Kraken2 and Bracken outputs. It provides rich, interactive visualisation and comparison of multiple samples.

2.1 Install Pavian in RStudio

In the RStudio Console:

if (!require(remotes)) { install.packages("remotes") }
remotes::install_github("fbreitwieser/pavian")

2.1.1 Launch Pavian

Run the following command in RStudio:

pavian::runApp(port=5000)

Pavian will then be available at http://127.0.0.1:5000 in the web browser of your choice.

2.1.2 Load Kraken2 report files

Using the Pavian interface, import the following files:

  • K1.kreport2
  • K2.kreport2
  • W1.kreport2

2.2 When to use Pavian instead of Krona

Use Pavian when:

  • You want to compare multiple samples interactively
  • You are already working within R or RStudio
  • You want richer filtering and comparison tools

Use Krona when:

  • You want a single self-contained HTML file
  • You need a lightweight visualisation with no R dependency
  • You want to easily share results by email or download