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test_make_otu_heatmap_html.py
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test_make_otu_heatmap_html.py
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#!/usr/bin/env python
#file test_make_otu_heatmap_html.py
__author__ = "Jesse Stombaugh"
__copyright__ = "Copyright 2011, The QIIME Project" #consider project name
__credits__ = ["Jesse Stombaugh", "Jose Carlos Clemente Litran",
"Jai Ram Rideout"] #remember to add yourself
__license__ = "GPL"
__version__ = "1.6.0"
__maintainer__ = "Jesse Stombaugh"
__email__ = "jesse.stombaugh@colorado.edu"
__status__ = "Release"
from numpy import array, log
import shutil
from shutil import rmtree
from os.path import join
from cogent.util.unit_test import TestCase, main
from qiime.make_otu_heatmap_html import (make_html_doc,create_javascript_array,\
filter_by_otu_hits,line_converter,\
get_log_transform,generate_heatmap_plots)
from qiime.util import create_dir,get_qiime_project_dir
from biom.table import table_factory
class TopLevelTests(TestCase):
"""Tests of top-level functions"""
def setUp(self):
"""define some top-level data"""
#self.col_header=['Sample1', 'Sample2']
#self.row_header=['OTU1','OTU2']
#self.otu_table=array([[0,0],[1,5]])
#self.lineages=[['Bacteria'],['Archaea']]
#self.data={}
#self.data['otu_counts']=self.col_header,self.row_header,self.otu_table,\
# self.lineages
self.output_dir='/tmp/'
otu_table_vals = array([[0,0],[1,5]])
#{(0,0):0.0,(1,0):1.0, (1,1):5.0}
self.otu_table = table_factory(otu_table_vals,
['Sample1', 'Sample2'],
['OTU1', 'OTU2'],
[None, None],
[{"taxonomy": ["Bacteria"]},
{"taxonomy": ["Archaea"]}])
filt_otu_table_vals = array([[1,5]])
#{(0,0):1.0, (0,1):5.0}
self.filt_otu_table = table_factory(filt_otu_table_vals,
['Sample1', 'Sample2'],
['OTU2'],
[None, None],
[{"taxonomy": ["Archaea"]}])
self.num_otu_hits=5
self._folders_to_cleanup=[]
def tearDown(self):
'''This function removes the generated files'''
map(rmtree,self._folders_to_cleanup)
def test_make_html_doc(self):
"""make_html_doc: create the web interface for otu heatmaps"""
obs = make_html_doc('./test/test_otu_count_table.js')
self.assertEqual(obs,exp_html_script)
def test_create_javascript_array(self):
"""create_javascript_array: takes a numpy array and generates a
javascript array"""
#self.rows=[['#OTU ID', 'OTU2'],['Sample1',1],['Sample2',5],\
# ['Consensus Lineage','Archaea']]
#obs=create_javascript_array(self.rows)
obs = create_javascript_array(self.filt_otu_table)
self.assertEqual(obs,exp_js_array)
def test_filter_by_otu_hits(self):
"""filter_by_otu_hits: filters the table by otu hits per otu"""
exp = array([['#OTU ID', 'OTU2'],['Sample1',1],['Sample2',5],\
['Consensus Lineage','Archaea;']])
#obs = filter_by_otu_hits(self.num_otu_hits,self.data)
obs = filter_by_otu_hits(self.num_otu_hits, self.otu_table)
#self.assertEqual(obs,exp)
#self.assertEqual( obs == self.filt_otu_table, True)
# see note in test_get_log_transform about this assert
self.assertEqual(obs._data.items(), self.filt_otu_table._data.items())
def test_get_log_transform(self):
#data = array([[0,1,2],[1000,0,0]])
#logdata = get_log_transform(data,eps=None)
# set zeros to 1/2s
#exp = log(array([[.5,1,2],[1000,.5,.5]]))
# translate to 0
#exp -= exp.min()
#self.assertFloatEqual(logdata, exp)
orig_data = array([[0,1,2],[1000,0,0]])
#{(0,1):1.0, (0,2):2,(1,0):1000.0}
orig_otu_table = table_factory(orig_data,
['Sample1', 'Sample2', 'Sample3'],
['OTU1', 'OTU2'],
[None, None, None],
[{"taxonomy": ["Bacteria"]},
{"taxonomy": ["Archaea"]}])
exp_data = array([[0,0.69314718,1.38629436],[7.60090246,0,0]])
#{(0,1):0.69314718, (0,2):1.38629436,(1,0):7.60090246}
exp_otu_table = table_factory(exp_data,
['Sample1', 'Sample2', 'Sample3'],
['OTU1', 'OTU2'],
[None, None, None],
[{"taxonomy": ["Bacteria"]},
{"taxonomy": ["Archaea"]}])
log_otu_table = get_log_transform(orig_otu_table, eps = None)
# comparing directly log_otu_table against exp_otu_table doesn't work,
# needs to be modified in the otu table object
self.assertFloatEqual(list(log_otu_table.iterSampleData()),
list(exp_otu_table.iterSampleData()))
def test_generate_heatmap_plots(self):
"""generate_heatmap_plots: create default output files"""
# create directories and move js files to verify everything works
# in the script file
dir_path=join(self.output_dir,'test')
create_dir(dir_path)
js_dir_path=join(dir_path,'js')
create_dir(js_dir_path)
self._folders_to_cleanup.append(dir_path)
qiime_dir=get_qiime_project_dir()
js_path=join(qiime_dir,'qiime/support_files/js')
shutil.copyfile(join(js_path,'overlib.js'), join(js_dir_path,'overlib.js'))
shutil.copyfile(join(js_path,'otu_count_display.js'), join(js_dir_path,'otu_count_display.js'))
shutil.copyfile(join(js_path,'jquery.js'), join(js_dir_path,'jquery.js'))
shutil.copyfile(join(js_path,'jquery.tablednd_0_5.js'), join(js_dir_path,'jquery.tablednd_0_5.js'))
# generate otu_table object
orig_data = array([[0,1,2],[1000,0,0]])
orig_otu_table = table_factory(orig_data,
['Sample1', 'Sample2', 'Sample3'],
['OTU1', 'OTU2'],
[None, None, None],
[{"taxonomy": ["Bacteria"]},
{"taxonomy": ["Archaea"]}])
# put in an OTU sort order and sample order
otu_sort=['OTU2','OTU1']
sample_sort=['Sample2','Sample1','Sample3']
num_otu_hits=3
# generate test files
generate_heatmap_plots(num_otu_hits, orig_otu_table, otu_sort,
sample_sort, dir_path, js_dir_path,
'test',fractional_values=False)
self.assertEqual(open(join(js_dir_path,'test.js'),'U').read(),
exp_js_output_file)
exp_js_array='''\
var OTU_table=new Array();\n\
var i=0;\n\
for (i==0;i<4;i++) {\n\
OTU_table[i]=new Array();}\n\
OTU_table[0][0]='#OTU ID';\n\
OTU_table[0][1]='OTU2';\n\
OTU_table[1][0]='Sample1';\n\
OTU_table[1][1]=1;\n\
OTU_table[2][0]='Sample2';\n\
OTU_table[2][1]=5;\n\
OTU_table[3][0]='Consensus Lineage';\n\
OTU_table[3][1]='Archaea';\n\
'''
exp_js_output_file="""\
var otu_num_cutoff=3; var OTU_table=new Array();
var i=0;
for (i==0;i<5;i++) {
OTU_table[i]=new Array();}
OTU_table[0][0]='#OTU ID';
OTU_table[0][1]='OTU2';
OTU_table[0][2]='OTU1';
OTU_table[1][0]='Sample2';
OTU_table[1][1]=0;
OTU_table[1][2]=1;
OTU_table[2][0]='Sample1';
OTU_table[2][1]=1000;
OTU_table[2][2]=0;
OTU_table[3][0]='Sample3';
OTU_table[3][1]=0;
OTU_table[3][2]=2;
OTU_table[4][0]='Consensus Lineage';
OTU_table[4][1]='Archaea';
OTU_table[4][2]='Bacteria';
"""
exp_html_script = \
r'''
<html>
<head>
<script type="text/javascript" src="js/overlib.js"></script>
<script type="text/javascript" src="./test/test_otu_count_table.js"></script>
<script type="text/javascript" src="js/otu_count_display.js"></script>
<script type="text/javascript" src="./js/jquery.js"></script>
<script type="text/javascript" src="./js/jquery.tablednd_0_5.js"></script>
<script type="text/javascript">
$(document).ready(function() {
$('#otu_table_body').tableDnD({
onDragStart: function(table, new_row) {
if (row==new_row.parentNode.rowIndex && is_selected==1){
change_sel_row=1;
}else{
old_row=new_row.parentNode.rowIndex;
change_sel_row=0;
}
},
onDrop: function(table, new_row) {
if (change_sel_row==1){
row=new_row.rowIndex;
}else if(old_row<row && new_row.rowIndex>row){
row=row-1;
}else if(old_row>row && new_row.rowIndex<row){
row=row+1;
}
},
dragHandle: "dragHandle"
});
var otu_cutoff=document.getElementById("otu_count_cutoff");
otu_cutoff.value=otu_num_cutoff;
});
</script>
<style type="text/css">
th.rotate{
white-space : nowrap;
-webkit-transform: rotate(-90deg) translate(20px, 0px);
-moz-transform: rotate(-90deg) translate(20px, 0px);
font-family:arial;
font-size:9px;
}
th.lineage{
white-space : nowrap;
text-align:left;
font-family:arial;
font-size:10px;
font-weight: bolder;
}
td.dragHandle{
white-space : nowrap;
text-align:left;
font-family:arial;
font-size:10px;
font-weight: bolder;
}
td{
white-space : nowrap;
font-family:arial;
font-size:10px;
text-align:center;
font-weight: bolder;
}
table{
border-spacing: 0;
text-align:center;
}
p{
text-align:left;
font-weight: normal;
}
</style>
</head>
<body>
<p>
Filter by Counts per OTU: <input type="text" id="otu_count_cutoff" value="">
<input type="button" onclick="javascript:create_OTU_intervals();" value="Sample ID">
<input type="button" onclick="javascript:write_taxon_heatmap();" value="Taxonomy">
</p>
<br><br><br><br><br><br>
<table id='otu_table_html'>
<thead id='otu_table_head'>
</thead>
<tbody id='otu_table_body'>
<tr><td class="dragHandle"></td>
</tr>
<tr><td class="dragHandle"></td>
</tr>
</tbody>
</table>
</body>
</html>'''
#run tests if called from command line
if __name__ == "__main__":
main()