Merge pull request #152 from ElDeveloper/issue_121_and_144

Changes for comparison plots

ChangeLog.md

@@ -18,13 +18,18 @@ Emperor 0.9.1 (changes since Emperor 0.9.0 go here)
 * Export to SVG your visualization.
 * Emperor now relies on QIIME 1.7.0.
 * Added option `--number_of_segments` to control the quality of all spheres
+* Add color pickers for connecting bars in coordinate comparison plots.
+* Add option to select a master set of coordinates when making a comparison plot.
 
 *Bug Fixes*
 
 * Fixes recenter camera not working.
 * Category names are sorted alphabetically.
 * Category names with non-alphanumeric characters are colored correctly now.
 * Biplots checkbox now accurately reflects status of biplot visiblity rather than opposite.
+* Comparison bars checkbox now accurately reflects status of the visiblity rather than opposite.
+* Scaling by percent explained now works with vectors and coordinate comparison plots.
+* Fixed bug where only the first bars in coordinate comparison plots could be hidden.
 
 Emperor 0.9.0 (14 May 2013)
 ===========================

emperor/format.py

@@ -307,13 +307,16 @@ def format_vectors_to_js(mapping_file_data, mapping_file_headers, coords_data,
 
     return ''.join(js_vectors_string)
 
-def format_comparison_bars_to_js(coords_data, coords_headers, clones):
+def format_comparison_bars_to_js(coords_data, coords_headers, clones,
+                                is_serial_comparison=True):
     """Format coordinates data to create a comparison plot
 
     Inputs:
     coords_data: numpy array with the replicated coordinates
     cooreds_headers: list with the headers for each of replicated coordinates
     clones: number of replicates in the coords_data and coords_headers
+    is_serial_comparison: whether the samples will be connected one after the
+    other (True) or all will originate in the first set of coordinates.
 
     Outputs:
     Javascript object that contains the data for the comparison plot
@@ -323,11 +326,19 @@ def format_comparison_bars_to_js(coords_data, coords_headers, clones):
     length.
     AssertionError if the number of clones doesn't concord with the samples
     being presented.
+
+    Unless the value of clones is > 0 this function will return an empty
+    javascript object initialization.
     """
 
     js_comparison_string = []
     js_comparison_string.append('\nvar g_comparisonPositions = new Array();\n')
 
+    if is_serial_comparison:
+        js_comparison_string.append('var g_isSerialComparisonPlot = true;\n')
+    else:
+        js_comparison_string.append('var g_isSerialComparisonPlot = false;\n')
+
     if clones:
         headers_length = len(coords_headers)
 
@@ -367,6 +378,9 @@ def format_emperor_html_footer_string(has_biplots=False, has_ellipses=False,
 
     has_biplots: whether the plot has biplots or not
     has_ellipses: whether the plot has ellipses or not
+    has_vectors: whether the plot has vectors or not
+    has_edges: whether the plot has edges between samples (comparison plot)
+
 
     This function will remove unnecessary GUI elements from index.html to avoid
     confusions i. e. showing an ellipse opacity slider when there are no
@@ -378,6 +392,7 @@ def format_emperor_html_footer_string(has_biplots=False, has_ellipses=False,
     optional_strings.append(if_(has_biplots, _BIPLOT_SPHERES_COLOR_SELECTOR,''))
     optional_strings.append(if_(has_biplots, _BIPLOT_VISIBILITY_SELECTOR, ''))
     optional_strings.append(if_(has_biplots, _TAXA_LABELS_SELECTOR, ''))
+    optional_strings.append(if_(has_edges, _EDGES_COLOR_SELECTOR, ''))
     optional_strings.append(if_(has_ellipses, _ELLIPSE_OPACITY_SLIDER, ''))
     optional_strings.append(if_(has_vectors, _VECTORS_OPACITY_SLIDER, ''))
     optional_strings.append(if_(has_edges, _EDGES_VISIBILITY_SELECTOR, ''))
@@ -454,10 +469,15 @@ def format_emperor_html_footer_string(has_biplots=False, has_ellipses=False,
 _EDGES_VISIBILITY_SELECTOR = """
             <br>
             <form name="edgesvisibility">
-            <input type="checkbox" onClick="toggleEdgesVisibility()">Edges Visibility</input>
+            <input type="checkbox" onClick="toggleEdgesVisibility()" checked>Edges Visibility</input>
             </form>
             <br>"""
 
+_EDGES_COLOR_SELECTOR = """
+            <tr><td><div id="edgecolorselector_a" class="colorbox" name="edgecolorselector_a"></div></td><td title="edgecolor_a">Edge Color Selector A</td></tr>
+            <tr><td><div id="edgecolorselector_b" class="colorbox" name="edgecolorselector_b"></div></td><td title="edgecolor_b">Edge Color Selector B</td></tr>
+"""
+
 _EMPEROR_FOOTER_HTML_STRING ="""document.getElementById("logo").style.display = 'none';
 document.getElementById("logotable").style.display = 'none';
 
@@ -566,16 +586,16 @@ def format_emperor_html_footer_string(has_biplots=False, has_ellipses=False,
             <table>
                 <tr><td><div id="axeslabelscolor" class="colorbox" name="axeslabelscolor"></div></td><td title="Axes Labels Color">Axes Labels Color</td></tr>
                 <tr><td><div id="axescolor" class="colorbox" name="axescolor"></div></td><td title="Axes Color Title">Axes Color</td></tr>
-                <tr><td><div id="rendererbackgroundcolor" class="colorbox" name="rendererbackgroundcolor"></div></td><td title="Background Color Title">Background Color</td></tr>
+                <tr><td><div id="rendererbackgroundcolor" class="colorbox" name="rendererbackgroundcolor"></div></td><td title="Background Color Title">Background Color</td></tr>%s
             </table>
-            <br>
-            <form name="settingsoptionscolor">
-            <input type="checkbox" onchange="toggleContinuousAndDiscreteColors(this)" id="discreteorcontinuouscolors" name="discreteorcontinuouscolors">  Use gradient colors</input>
-            </form>
             <div id="pcoaviewoptions" class="">
                 <br>
                 <input id="reset" class="button" type="submit" value="Recenter Camera" style="" onClick="resetCamera()">
-                <br>%s%s%s
+                <br>
+                <br>
+                <form name="settingsoptionscolor">
+                <input type="checkbox" onchange="toggleContinuousAndDiscreteColors(this)" id="discreteorcontinuouscolors" name="discreteorcontinuouscolors">  Use gradient colors</input>
+                </form>%s%s%s
                 <br>
                 <label for="sphereopacity" class="text">Sphere Opacity</label>
                 <label id="sphereopacity" class="slidervalue"></label>

emperor/sort.py

@@ -11,8 +11,8 @@
 __email__ = "yoshiki89@gmail.com"
 __status__ = "Development"
 
-
 from numpy import zeros
+from re import compile, search
 
 def sort_taxa_table_by_pcoa_coords(coords_header, otu_table, otu_header):
     """Sort and match the samples in the otu table and in the coordinates data
@@ -48,3 +48,40 @@ def sort_taxa_table_by_pcoa_coords(coords_header, otu_table, otu_header):
             sorted_otu_headers.append(element)
 
     return sorted_otu_headers, sorted_otu_table
+
+def sort_comparison_filenames(coord_fps):
+    """Pass in a list of file names and sort them using the suffix
+
+    Input:
+    coord_fps: list of filenames with the format something_something_qX.txt
+    where X is the index of the file.
+
+    Output:
+    Returns a sorted version of the list that was passed in where the strings
+    are sorted according to the suffix they have, if the string doesn't have
+    a suffix it will be added to the beginning of the list.
+    """
+
+    if coord_fps == []:
+        return []
+
+    def _get_suffix(fp):
+        """Gets the number in the suffix for a string using a regex"""
+        # any alphanumeric set of characters proceeded by a 'q', a number, a dot
+        # & a txt extension at the end of the line. Take for example 
+        # bray_curtis_q1.txt or unifrac_q11.txt
+        re = compile(r'(\w+)_q([0-9]+).txt$')
+        tmatch = search(re, fp)
+
+        try:
+            number = tmatch.group(2)
+        # if the regex doesn't match then put it at the beginning
+        except (IndexError, AttributeError):
+            number = -1
+
+        return float(number)
+
+    # the key function retrieves the suffix number for the function to sort
+    # according to it's floating point representation i. e. the cast to float
+    return sorted(coord_fps, key=_get_suffix)
+