Emperor uses two main files as inputs, a mapping file and a coordinates file, here we will describe their structure.
A mapping file refers to the additional information collected about your samples, some common examples are body site, collection time, pH, latitude, longitude, etc. This information is used by Emperor to color and modify visual aspects of your plot in a systematic way.
Mapping files should conform to the format as described by QIIME. Note that the only required column is SampleID, if this column is not present the file will not be parsed correctly and the script will bring up an error.
Coordinates files describe the position in which each of the samples should be placed in space, as of version 0.9.4-dev there are two different file formats that are accepted by Emperor:
Classic Format
This format is tab-delimited and must include the following information ( versions of QIIME <= 1.8.0 generate this file when you execute principal_coordinates.py):
See the example below that presents a dataset where 5 samples were included.
pc vector number 1 2 3 4 5
PC.636 0.333514620475 0.081687 0.25081 0.103746 2.50106743521e-09
PC.635 0.258145479886 -0.22437 -0.25446 -0.0290044 2.50106743521e-09
PC.356 -0.270663791669 -0.23983 0.18965 -0.118931 2.50106743521e-09
PC.481 -0.0437436047686 0.30751 -0.077078 -0.20627 2.50106743521e-09
PC.354 -0.277252703922 0.074945 -0.10898 0.245681 2.50106743521e-09
eigvals 0.329912543767 0.2147172 0.1815366 0.1261003 -3.127915774e-17
% variation explained 38.68853 25.18276 21.2717 14.85772 3.667478e-15
scikit-bio Ordination Results
Emperor is also capable of parsing files generated by scikit-bio’s OrdinationResults class.