emperor.core.Emperor¶

class emperor.core.Emperor(ordination, mapping_file_data, mapping_file_headers)¶

Display principal coordinates analysis plots

Use this object to interactively display a PCoA plot using the Emperor GUI. IPython provides a rich display system that will let you display a plot inline, without the need of creating a temprorary file or having to write to disk.

Parameters:	ordination: skbio.maths.stats.ordination.OrdinationResults Object containing the computed values for an ordination method in scikit-bio. mapping_file_data: list of list objects Metadata mapping file used to color the plot. mapping_file_headers: list of str objects List of strings representing the header names of the mapping_file_data. All names should be unique.

Notes

This object currently does not support the full range of actions that the GUI does support and should be considered experimental at the moment.

References

[R2]	EMPeror: a tool for visualizing high-throughput microbial community data Vazquez-Baeza Y, Pirrung M, Gonzalez A, Knight R. Gigascience. 2013 Nov 26;2(1):16.

Examples

Create an Emperor object and display it from the IPython notebook:

>>> data = [['PC.354', 'Control', '20061218', 'Control_mouse_I.D._354'],
... ['PC.355', 'Control', '20061218', 'Control_mouse_I.D._355'],
... ['PC.356', 'Control', '20061126', 'Control_mouse_I.D._356'],
... ['PC.481', 'Control', '20070314', 'Control_mouse_I.D._481'],
... ['PC.593', 'Control', '20071210', 'Control_mouse_I.D._593'],
... ['PC.607', 'Fast', '20071112', 'Fasting_mouse_I.D._607'],
... ['PC.634', 'Fast', '20080116', 'Fasting_mouse_I.D._634'],
... ['PC.635', 'Fast', '20080116', 'Fasting_mouse_I.D._635'],
... ['PC.636', 'Fast', '20080116', 'Fasting_mouse_I.D._636']]
>>> headers = ['SampleID', 'Treatment', 'DOB', 'Description']
>>> ordination = OrdinationResults.read('unweighted_unifrac_pc.txt')

Now import the Emperor object and display it using IPython, note that this call will have no effect under an interactive Python session:

>>> from emperor import Emperor
>>> Emperor(ordination, data, headers)