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Merge pull request #19 from martinSergeant/master
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update
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@zheminzhou
zheminzhou committed Aug 8, 2017
2 parents 71f073d + 9325a1d commit 9797e11
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163 changes: 80 additions & 83 deletions MSTree_holder.html
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Original file line number Diff line number Diff line change
Expand Up @@ -72,7 +72,7 @@
<div>
<a class='show-tooltip' title="EnteroBase" href="https://enterobase.warwick.ac.uk" target = '_blank'><img src="static/js/img/enterobase.png" alt="Enterobase" style="width:40px;height:45px;"></a>&nbsp;&nbsp;|&nbsp;&nbsp;
<a class='show-tooltip' title='GrapeTree GitHub repository' href="https://github.com/martinSergeant/EnteroMSTree" target = '_blank'><img src="static/js/img/GrapeTree.PNG" alt="GrapeTree" style="width:40px;height:50px;"></a>&nbsp;&nbsp;|&nbsp;&nbsp;
<a class='show-tooltip' title='Help' href="https://bitbucket.org/enterobase/enterobase-web/wiki/GrapeTree" target = '_blank'><img src="static/js/img/question.PNG" alt="Help" style="width:40px;height:50px;"></a>
<a class='show-tooltip' title='Help' href="https://bitbucket.org/enterobase/enterobase-web/wiki/GrapeTree" target = '_blank'><img src="static/js/img/question.PNG" alt="Help" style="width:20px;height:24px;"></a>
<h3 id="headertag" style="font-family: times, serif; font-size:12pt; font-style:italic">GrapeTree</h3>
</div>
<br>
Expand All @@ -82,13 +82,12 @@ <h3 id="headertag" style="font-family: times, serif; font-size:12pt; font-style:
<div id ='load-panel'>
<button title='Handles trees, profiles and metadata files' id = 'button-load-nwk' class = 'show-tooltip'> Load Files</button>
<span class="glyphicon glyphicon-question-sign" style="float:right;margin-right:5px" onclick="getHelpBox('load_files');"></span>
<br>
<hr>
</div>
<div id='save-panel'>
<button id ="save-tree-json">Save GrapeTree</button>
<span class="glyphicon glyphicon-question-sign" style="float:right;margin-right:5px" onclick="getHelpBox('save_grapetree');"></span><br><br>
<button id ="save-tree-nwk">Save as Newick Tree</button><br><br>
<span class="glyphicon glyphicon-question-sign" style="float:right;margin-right:5px" onclick="getHelpBox('save_grapetree');"></span><br>
<button id ="save-tree-nwk">Save as Newick Tree</button><br>
<button id ="mst-download-svg">Download SVG</button><br>
</div>
</div>
Expand All @@ -97,99 +96,97 @@ <h3 id="headertag" style="font-family: times, serif; font-size:12pt; font-style:
<div class ='panel-heading mst-menu-title' id= 'tree-menu'> <b id>Tree Layout</b><span id = 'tree-menu-icon' class='glyphicon glyphicon-menu-right'> </span></div>
<div class = "panel-body" id ='tree-menu-panel' style='padding:0px;' ><br>
<button id = 'button-goback' style='margin-left:15px;' onclick='loadMSTree(tree_raw);if(current_metadata_file) {loadMetadataFile(current_metadata_file[0], current_metadata_file[1]);}'> Unmodified tree</button>
<span class="glyphicon glyphicon-question-sign" style="float:right;margin-right:5px" onclick="getHelpBox('tree_layout');"></span>
<br><br>
<span class="glyphicon glyphicon-question-sign" style="float:right;margin-right:15px" onclick="getHelpBox('tree_layout');"></span>
<br>
<button id = 'button-refresh' style='margin-left:15px;' > Static Redraw </button>
<br><br>
<br>
<button id ="center-graph-button" style='margin-left:15px;' >Centre Tree</button>
<br>
<label><input id ='show-node-tooltip' style='margin-left:15px;' type="checkbox" checked /> Show Tooltips</label>
<br>
<hr>
<p align = 'center' style='margin-left: 3em;' >
<div id="rotation-div"><label> Drag Icon to Rotate:&nbsp;</label>
<p align = 'center'>
<label> Drag Icon to Rotate:&nbsp;</label>
<span id="rotation-icon" class="glyphicon glyphicon-refresh"></span>
</div>
<br>
<label>Zoom:&nbsp;</label>
<span onclick= "javascript:the_tree.setScale(1.1,true)" class=' zoom-icon glyphicon glyphicon-zoom-in'></span>
<span onclick= "javascript:the_tree.setScale(0.9,true)"class='zoom-icon glyphicon glyphicon-zoom-out'></span>
</p>
<div class='panel panel-default'>
<div class ='panel-heading mst-menu-title' id= 'mst-node-menu'> <b id>Node Style</b><span id = 'mst-node-menu-icon' class="glyphicon glyphicon-menu-right"></span></div>
<div class = "panel-body" id ='mst-node-menu-panel' >
<label>Colour By:</label>
<br>
<select style="width:140px" id= 'metadata-select'>
<option value='nothing'>No category</option></select>
<hr>
<label><input id ='show-node-labels'type="checkbox" checked /> Show Labels</label>
<span class="glyphicon glyphicon-question-sign" style="float:right;margin-right:5px" onclick="getHelpBox('show_labels');"></span>
<br><br>
<label>Font Size:</label>
<br>
<div id = "slider-node-fontsize" class = "slider-class"></div><input type='text' style='width:20px;height:15px' id ='spinner-node-fontsize' class='spin-group'><br>
<label>Label Text</label>
<select id = 'node-label-text'></select><br><br><hr>
<span class="glyphicon glyphicon-question-sign" style="float:right;margin-right:5px" onclick="getHelpBox('node_size');"></span>
<div >
<span onclick="$('#spinner-nodesize').spinner('value', 100)" class='glyphicon glyphicon-fast-backward'></span><label>&nbsp;&nbsp;Node Size (%)</label><br>
<div id = "slider-nodesize" class ="slider-class"></div><input type='text' style='width:39px;height:15px' id ='spinner-nodesize' class='spin-group'>
</div>

<div class="show-tooltip" title="Node size relative to number of strains">
<span onclick="$('#spinner-relative-nodesize').spinner('value', 100)" class='glyphicon glyphicon-fast-backward'></span><label>&nbsp;&nbsp; Relative Scaling (%)</label><br>
<div id = "slider-relative-nodesize" class ="slider-class"></div><input type='text' style='width:39px;height:15px' id ='spinner-relative-nodesize' class='spin-group'>
</div><br>
<hr>
<label>Search in Label</label>
<br>
<input size="11" id ='search-metadata-input'><span id ='search-metadata-icon' class='add-data-icon glyphicon glyphicon-search'></span>
<br>
<label><input id ='show-individual-segments' type="checkbox" /> Show Pie Chart</label>
<br>
</div>
</div>
<div class='panel panel-default'>
<div class ='panel-heading mst-menu-title' id= 'mst-link-menu'> <b id>Branch Style</b><span id = 'mst-link-menu-icon' class='glyphicon glyphicon-menu-right'> </span></div>
<div class = "panel-body" id ='mst-link-menu-panel'>
<label><input id ='show-link-labels'type="checkbox" /> Show Labels</label>
<span class="glyphicon glyphicon-question-sign" style="float:right;margin-right:5px" onclick="getHelpBox('branch_labels');"></span>
<br>
<label>Font Size:</label>
<br>
<div id = "slider-linkfontsize" class = "slider-class"></div><input type='text' style='width:20px;height:15px' id ='spinner-linkfontsize' class='spin-group'>
<br>
<div>
<span onclick="$('#spinner-linklength').spinner('value', 100)" class='glyphicon glyphicon-fast-backward'></span><label>&nbsp;&nbsp; Scaling (%)</label><br>
<div id = "slider-linklength" class ="slider-class"> </div><input type='text' style='width:39px;height:15px' id ='spinner-linklength' class='spin-group'>
</div>

<div class="show-tooltip" title="Collapse branches below a certain value">
<span onclick="$('#spinner-collapse-nodes').spinner('value', 0)" class='glyphicon glyphicon-fast-backward'></span><label>&nbsp;&nbsp;Collapse Branches</label><br>
<div id = "slider-collapse-nodes" class ="slider-class"></div><input type='text' style='width:39px;height:15px' id ='spinner-collapse-nodes' class='spin-group'>
<div class='panel panel-default sub-panel'>
<div class ='panel-heading mst-menu-title' id= 'mst-node-menu'> <b id>Node Style</b><span id = 'mst-node-menu-icon' class="glyphicon glyphicon-menu-right"></span></div>
<div class = "panel-body" id ='mst-node-menu-panel' >
<label>Colour By:</label>
<br>
<select style="width:160px" id= 'metadata-select'>
<option value='nothing'>No category</option></select>
<hr>
<label><input id ='show-node-labels'type="checkbox" checked /> Show Labels</label>
<span class="glyphicon glyphicon-question-sign" style="float:right;margin-right:5px" onclick="getHelpBox('show_labels');"></span>
<br>
<label>Font Size:</label>
<br>
<div id = "slider-node-fontsize" class = "slider-class"></div><input type='text' style='width:20px;height:15px' id ='spinner-node-fontsize' class='spin-group'><br>
<label>Label Text</label>
<select style='width:160px' id = 'node-label-text'></select><hr>
<span class="glyphicon glyphicon-question-sign" style="float:right;margin-right:5px" onclick="getHelpBox('node_size');"></span>
<div >
<span onclick="$('#spinner-nodesize').spinner('value', 100)" class='glyphicon glyphicon-fast-backward'></span><label>&nbsp;&nbsp;Node Size (%)</label><br>
<div id = "slider-nodesize" class ="slider-class"></div><input type='text' id ='spinner-nodesize' class='spin-group'>
</div>

<div class="show-tooltip" title="Node size relative to number of strains">
<span onclick="$('#spinner-relative-nodesize').spinner('value', 100)" class='glyphicon glyphicon-fast-backward'></span><label>&nbsp;&nbsp;Relative Scaling (%)</label><br>
<div id = "slider-relative-nodesize" class ="slider-class"></div><input type='text' id ='spinner-relative-nodesize' class='spin-group'>
</div>
<hr>
<label>Search in Label</label>
<br>
<input size="11" id ='search-metadata-input'><span id ='search-metadata-icon' class='add-data-icon glyphicon glyphicon-search'></span>
<br>
<label><input id ='show-individual-segments' type="checkbox" /> Show Pie Chart</label>
<br>
</div>
<label><input id ='link-log-scale'type="checkbox" />Log Scale</label>
<br>
<hr>
<label>For branches <br>longer than:</label>
<input type='text' style='width:35px;height:15px' id ='spinner-hide-link-length' class='spin-group'>
<span class="glyphicon glyphicon-question-sign" style="float:right;margin-right:5px" onclick="getHelpBox('branch_cutoff');"></span>
<table><tbody><tr>
<td>
<div style="opacity: 1;"><input type="radio" id="handle-long-branch-display" name="handle-long-branch" value="display" checked="" style="opacity: 1;">Display</div>
</td>
<td style="padding-left:10px">
<div style="opacity: 1;"><input type="radio" id="handle-long-branch-hide" name="handle-long-branch" value="hide" style="opacity: 1;">Hide</div>
</td>
<td style="padding-left:10px">
<div style="opacity: 1;"><input type="radio" id="handle-long-branch-cap" name="handle-long-branch" value="cap" style="opacity: 1;">Shorten</div>
</td>
</tr></tbody></table>
</div>
</div>
<div class='panel panel-default sub-panel'>
<div class ='panel-heading mst-menu-title' id= 'mst-link-menu'> <b id>Branch Style</b><span id = 'mst-link-menu-icon' class='glyphicon glyphicon-menu-right'> </span></div>
<div class = "panel-body" id ='mst-link-menu-panel'>
<label><input id ='show-link-labels'type="checkbox" /> Show Labels</label>
<span class="glyphicon glyphicon-question-sign" style="float:right;margin-right:5px" onclick="getHelpBox('branch_labels');"></span>
<br>
<label>Font Size:</label>
<br>
<div id = "slider-linkfontsize" class = "slider-class"></div><input type='text' style='width:20px;height:15px' id ='spinner-linkfontsize' class='spin-group'>
<br>
<div>
<span onclick="$('#spinner-linklength').spinner('value', 100)" class='glyphicon glyphicon-fast-backward'></span><label>&nbsp;&nbsp;Scaling (%)</label><br>
<div id = "slider-linklength" class ="slider-class"> </div><input type='text' id ='spinner-linklength' class='spin-group'>
</div>

<div class="show-tooltip" title="Collapse branches below a certain value">
<span onclick="$('#spinner-collapse-nodes').spinner('value', 0)" class='glyphicon glyphicon-fast-backward'></span><label>&nbsp;&nbsp;Collapse Branches</label><br>
<div id = "slider-collapse-nodes" class ="slider-class"></div><input type='text' id ='spinner-collapse-nodes' class='spin-group'>
</div>
<label><input id ='link-log-scale'type="checkbox" />Log Scale</label>
<hr>
<span class="glyphicon glyphicon-question-sign" style="float:right;margin-right:5px" onclick="getHelpBox('branch_cutoffs');"></span>
<label>For branches <br> longer than:<input type='text' id ='spinner-hide-link-length' class='spin-group'></label>
<table><tbody><tr>
<td>
<div style="opacity: 1;"><input type="radio" id="handle-long-branch-display" name="handle-long-branch" value="display" checked="" style="opacity: 1;">Display</div>
</td>
<td style="padding-left:10px">
<div style="opacity: 1;"><input type="radio" id="handle-long-branch-hide" name="handle-long-branch" value="hide" style="opacity: 1;">Hide</div>
</td>
<td style="padding-left:10px">
<div style="opacity: 1;"><input type="radio" id="handle-long-branch-cap" name="handle-long-branch" value="cap" style="opacity: 1;">Shorten</div>
</td>
</tr></tbody></table>
</div>
</div>
</div>
</div>


<div class='panel panel-default'>
<div class ='panel-heading mst-menu-title' id= 'mst-layout-menu'> <b id>Rendering</b><span id = 'mst-layout-menu-icon' class="glyphicon glyphicon-menu-right"></span></div>
<div class = "panel-body" id ='mst-layout-menu-panel'>
Expand Down Expand Up @@ -315,7 +312,7 @@ <h3 id="headertag" style="font-family: times, serif; font-size:12pt; font-style:
$(this).parent().dialog().dialog("close");
});

var notification = "<p style='font-size:10'> Some browsers allow you to select a folder after you click the 'Save' Button.<br><br> Whereas many browsers, such as Chrome, by default save the downloaded file into:<br><b>Windows</b>: <code>'&#92;Users&#92;&lt;username&gt;&#92;Downloads'</code><br><b>Mac</b>: <code>'/Users/&lt;username&gt;/Downloads'</code><br><b>Linux</b>: <code>'home/&lt;username&gt;/Downloads'</code><br><br></p>";
var notification = "<p style='font-size:10'> Some browsers allow you to select a folder after you click the 'Save' Button.<br> Whereas many browsers, such as Chrome, by default save the downloaded file into:<br><b>Windows</b>: <code>'&#92;Users&#92;&lt;username&gt;&#92;Downloads'</code><br><b>Mac</b>: <code>'/Users/&lt;username&gt;/Downloads'</code><br><b>Linux</b>: <code>'home/&lt;username&gt;/Downloads'</code><br></p>";
var filenamebar = $("<input title='Suffix will be automatically added in some browsers if you have got a file with the same name.' type='text' id ='filename' value='"+suggested_name+"'>");
//the actual dailog box
$("<div id ='savedailog'></div>")
Expand Down
41 changes: 22 additions & 19 deletions MSTrees.py
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Original file line number Diff line number Diff line change
Expand Up @@ -243,25 +243,28 @@ def NJ(names, profiles, missing_data='pair_delete', **params) :
taxon.label = names[int(taxon.label)]
return tree

def nonredundant(names, profiles) :
encoded_profile = np.array([np.unique(p, return_inverse=True)[1]+1 for p in profiles.T]).T
encoded_profile[(profiles == '-') | (profiles == '0')] = 0

names = names[np.lexsort(encoded_profile.T)]
profiles = encoded_profile[np.lexsort(encoded_profile.T)]
uniqueness = np.concatenate([[1], np.sum(np.diff(profiles, axis=0) != 0, 1) > 0])

embeded = {names[0]:[]}
embeded_group = embeded[names[0]]
for n, u in zip(names, uniqueness) :
if u == 0 :
embeded_group.append(n)
else :
embeded[n] = [n];
embeded_group = embeded[n];
names = names[uniqueness>0]
profiles = profiles[uniqueness>0]
return names, profiles, embeded
def nonredundant(names, profiles) :
encoded_profile = np.array([np.unique(p, return_inverse=True)[1]+1 for p in profiles.T]).T
encoded_profile[(profiles == '-') | (profiles == '0')] = 0

names = names[np.lexsort(encoded_profile.T)]
profiles = encoded_profile[np.lexsort(encoded_profile.T)]
presence = (np.sum(profiles > 0, 1) > 0)
names, profiles = names[presence], profiles[presence]

uniqueness = np.concatenate([[1], np.sum(np.diff(profiles, axis=0) != 0, 1) > 0])

embeded = {names[0]:[]}
embeded_group = embeded[names[0]]
for n, u in zip(names, uniqueness) :
if u == 0 :
embeded_group.append(n)
else :
embeded[n] = [n]
embeded_group = embeded[n]
names = names[uniqueness>0]
profiles = profiles[uniqueness>0]
return names, profiles, embeded

def backend(**parameters) :
'''
Expand Down
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