Merge pull request #281 from ElDeveloper/core

ENH: Add Emperor class

ChangeLog.md

@@ -13,6 +13,7 @@ Emperor 0.9.3-dev (changes since Emperor 0.9.2 go here)
 * Add toggle visible button (`Invert Selected`) under the `Visibility` tab, this button will change hidden categories to visible and vice-versa.
 * Supports both NumPy 1.7 and 1.8.
 * Depends on scikit-bio-dev.
+* Emperor provides a Python object that is IPython aware (emperor.Emperor) that will display a usable plot from within the IPython notebook.
 
 *Bug Fixes*
 

emperor/__init__.py

@@ -10,4 +10,6 @@
 __email__ = "antgonza@gmail.com"
 __status__ = "Development"
 
-__all__ = ['biplots', 'format', 'filter', 'sort', 'util']
+from emperor.core import Emperor
+
+__all__ = ['Emperor', 'biplots', 'format', 'filter', 'sort', 'util']

emperor/core.py

@@ -0,0 +1,143 @@
+r"""
+Emperor 3D PCoA viewer
+======================
+
+This module provides an Object to interact and visualize an Emperor plot
+from the IPython notebook.
+
+Classes
+-------
+.. autosummary::
+    Emperor
+
+"""
+from __future__ import division
+
+from emperor.format import (format_mapping_file_to_js, format_pcoa_to_js,
+                            format_taxa_to_js, format_vectors_to_js,
+                            format_comparison_bars_to_js,
+                            EMPEROR_HEADER_HTML_STRING,
+                            format_emperor_html_footer_string)
+
+# we are going to use this remote location to load external resources
+RESOURCES_URL = 'http://emperor.colorado.edu/master/make_emperor/emperor_outpu\
+t/emperor_required_resources'
+
+__author__ = "Yoshiki Vazquez Baeza"
+__copyright__ = "Copyright 2013, The Emperor Project"
+__credits__ = ["Yoshiki Vazquez Baeza"]
+__license__ = "BSD"
+__version__ = "0.9.3-dev"
+__maintainer__ = "Yoshiki Vazquez Baeza"
+__email__ = "yoshiki89@gmail.com"
+__status__ = "Development"
+
+class Emperor(object):
+    """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.
+
+    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.from_file('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)
+
+    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
+    ----------
+    .. [1] 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.
+
+    """
+    def __init__(self, ordination, mapping_file_data, mapping_file_headers):
+        self.ordination = ordination
+        self.mapping_file_data = mapping_file_data
+        self.mapping_file_headers = mapping_file_headers
+        self.ids = [s[0] for s in mapping_file_data]
+        self._html = None
+
+    def __str__(self):
+        if self._html is None:
+            self._make_emperor()
+        return self._html
+
+    def _repr_html_(self):
+        """Used to be displayed in the IPython notebook"""
+
+        # we import here as IPython shouldn't be a dependency of Emperor
+        # however if this method is called it will be from an IPython notebook
+        # otherwise the developer is responsible for calling this method
+        from IPython.display import display, HTML
+
+        # this provides a string representation that's independent of the
+        # filesystem, it will instead retrieve them from the official website
+        output = str(self).replace('emperor_required_resources',
+                                   RESOURCES_URL)
+
+        # thanks to the IPython devs for helping me figure this one out
+        return display(HTML(output), metadata=dict(isolated=True))
+
+    def _make_emperor(self):
+        """Private method to build an Emperor HTML string"""
+        pcoa_string = format_pcoa_to_js(self.ids,
+                                        self.ordination.site,
+                                        self.ordination.eigvals,
+                                        self.ordination.proportion_explained)
+
+        # we pass the mapping file headers twice so nothing is filtered out
+        mf_string = format_mapping_file_to_js(self.mapping_file_data,
+                                              self.mapping_file_headers,
+                                              self.mapping_file_headers)
+
+        # A lot of this is going to be empty because we don't really need any
+        # of it
+        footer = format_emperor_html_footer_string(False, False, False, False)
+        taxa = format_taxa_to_js([], [], [])
+        bars = format_comparison_bars_to_js([], [], 0)
+        vectors = format_vectors_to_js([], [], [], [], None)
+
+        # build the HTML string
+        output = [EMPEROR_HEADER_HTML_STRING, mf_string, pcoa_string, taxa,
+                  bars, vectors, footer]
+
+        # add the remote resources
+        _emperor = '\n'.join(output)
+
+        self._html = _emperor
+