Emperor is a next-generation tool for the analysis and visualization of large microbial ecology datasets; amongst many features Emperor provides a modern user interface that will rapidly adjust to your daily workflow.

To start using Emperor, please refer to the installation notes.

The main interface to create Emperor visualizations is the make_emperor.py script, inputing a mapping file and a PCoA data file, will generate an Emperor graphical user interface to analyze and visualize your data.

If you have a QIIME compliant mapping file and a PCoA file, try the following command from a terminal session:

make_emperor.py -i unweighted_unifrac_pc.txt -m mapping_file.txt

That command will create a new directory called emperor, there you will find a file called index.html open it with Google Chrome to start visualizing and interacting with your data.

Similarly if you have a study expressed over a gradient, for example a study where you have multiple samples over time, you can use this metadata with your visualization using the -a option:

make_emperor.py -i unweighted_unifrac_pc_time.txt -m mapping_with_time.txt -a TIMEPOINT

Some build examples are bundled with every Emperor repository, you can begin exploring some sample data using Google Chrome:

• To see an example of a simple PCoA plot, see this link.
• To see an example of a Jackknifed plot, see this link.
• To see an example of a PCoA Biplot, see this link.
• To see an example of a PCoA plot with connecting lines between samples, see this link.
• To see an example of a PCoA plot with connecting lines between samples and an explicit axis, see this link.