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-rw-r--r--wqflask/base/data_set.py4
-rw-r--r--wqflask/base/mrna_assay_tissue_data.py14
-rw-r--r--wqflask/tests/unit/wqflask/correlation/test_correlation_gn3.py14
-rw-r--r--wqflask/wqflask/correlation/correlation_functions.py6
-rw-r--r--wqflask/wqflask/correlation/correlation_gn3_api.py205
-rw-r--r--wqflask/wqflask/correlation/show_corr_results.py2
-rw-r--r--wqflask/wqflask/templates/test_correlation_page.html159
-rw-r--r--wqflask/wqflask/views.py11
8 files changed, 405 insertions, 10 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index e20f2f98..75ddf278 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -124,6 +124,7 @@ class DatasetType:
self.datasets[short_dataset_name] = new_type
except Exception: # Do nothing
pass
+
self.redis_instance.set("dataset_structure",
json.dumps(self.datasets))
self.data = data
@@ -165,6 +166,7 @@ class DatasetType:
if t in ['pheno', 'other_pheno']:
group_name = name.replace("Publish", "")
+
results = g.db.execute(sql_query_mapping[t] % group_name).fetchone()
if results:
self.datasets[name] = dataset_name_mapping[t]
@@ -646,6 +648,8 @@ class DataSet:
"Dataset {} is not yet available in GeneNetwork.".format(self.name))
pass
+
+
def get_trait_data(self, sample_list=None):
if sample_list:
self.samplelist = sample_list
diff --git a/wqflask/base/mrna_assay_tissue_data.py b/wqflask/base/mrna_assay_tissue_data.py
index 882ae911..8f8e2b0a 100644
--- a/wqflask/base/mrna_assay_tissue_data.py
+++ b/wqflask/base/mrna_assay_tissue_data.py
@@ -6,6 +6,7 @@ from utility import db_tools
from utility import Bunch
from utility.db_tools import escape
+from gn3.db_utils import database_connector
from utility.logger import getLogger
@@ -45,16 +46,18 @@ class MrnaAssayTissueData:
and t.Mean = x.maxmean;
'''.format(in_clause)
- results = g.db.execute(query).fetchall()
- lower_symbols = []
+ # lower_symbols = []
+ lower_symbols = {}
for gene_symbol in gene_symbols:
+ # lower_symbols[gene_symbol.lower()] = True
if gene_symbol != None:
- lower_symbols.append(gene_symbol.lower())
-
+ lower_symbols[gene_symbol.lower()] = True
+ results = list(g.db.execute(query).fetchall())
for result in results:
symbol = result[0]
- if symbol.lower() in lower_symbols:
+ if symbol is not None and lower_symbols.get(symbol.lower()):
+
symbol = symbol.lower()
self.data[symbol].gene_id = result.GeneId
@@ -83,6 +86,7 @@ class MrnaAssayTissueData:
WHERE TissueProbeSetData.Id IN {} and
TissueProbeSetXRef.DataId = TissueProbeSetData.Id""".format(db_tools.create_in_clause(id_list))
+
results = g.db.execute(query).fetchall()
for result in results:
if result.Symbol.lower() not in symbol_values_dict:
diff --git a/wqflask/tests/unit/wqflask/correlation/test_correlation_gn3.py b/wqflask/tests/unit/wqflask/correlation/test_correlation_gn3.py
new file mode 100644
index 00000000..e1bd6d86
--- /dev/null
+++ b/wqflask/tests/unit/wqflask/correlation/test_correlation_gn3.py
@@ -0,0 +1,14 @@
+"""this module contains tests for code used in integrating to gn3 api"""
+from unittest import TestCase
+from base.data_set import create_dataset
+
+class TestCorrelation(TestCase):
+
+ def test_create_dataset(self):
+ """test for creating datasets"""
+
+ pass
+ def test_fetch_dataset_info(self):
+ """test for fetching dataset info data"""
+
+ pass
diff --git a/wqflask/wqflask/correlation/correlation_functions.py b/wqflask/wqflask/correlation/correlation_functions.py
index 0f24241a..2d25fbd8 100644
--- a/wqflask/wqflask/correlation/correlation_functions.py
+++ b/wqflask/wqflask/correlation/correlation_functions.py
@@ -82,6 +82,6 @@ def cal_zero_order_corr_for_tiss(primaryValue=[], targetValue=[], method='pearso
def get_trait_symbol_and_tissue_values(symbol_list=None):
tissue_data = MrnaAssayTissueData(gene_symbols=symbol_list)
-
- if len(tissue_data.gene_symbols):
- return tissue_data.get_symbol_values_pairs()
+ if len(tissue_data.gene_symbols) >0:
+ results = tissue_data.get_symbol_values_pairs()
+ return results
diff --git a/wqflask/wqflask/correlation/correlation_gn3_api.py b/wqflask/wqflask/correlation/correlation_gn3_api.py
new file mode 100644
index 00000000..98d52591
--- /dev/null
+++ b/wqflask/wqflask/correlation/correlation_gn3_api.py
@@ -0,0 +1,205 @@
+"""module that calls the gn3 api's to do the correlation """
+import json
+
+from wqflask.correlation import correlation_functions
+
+from base import data_set
+
+from base.trait import create_trait
+from base.trait import retrieve_sample_data
+
+from gn3.computations.correlations import compute_all_sample_correlation
+from gn3.computations.correlations import map_shared_keys_to_values
+from gn3.computations.correlations import compute_all_lit_correlation
+from gn3.computations.correlations import compute_tissue_correlation
+from gn3.db_utils import database_connector
+
+
+def create_target_this_trait(start_vars):
+ """this function creates the required trait and target dataset for correlation"""
+
+ this_dataset = data_set.create_dataset(dataset_name=start_vars['dataset'])
+ target_dataset = data_set.create_dataset(
+ dataset_name=start_vars['corr_dataset'])
+ this_trait = create_trait(dataset=this_dataset,
+ name=start_vars['trait_id'])
+ sample_data = ()
+ return (this_dataset, this_trait, target_dataset, sample_data)
+
+
+def process_samples(start_vars, sample_names, excluded_samples=None):
+ """process samples"""
+ sample_data = {}
+ if not excluded_samples:
+ excluded_samples = ()
+ sample_vals_dict = json.loads(start_vars["sample_vals"])
+ for sample in sample_names:
+ if sample not in excluded_samples:
+ val = sample_vals_dict[sample]
+ if not val.strip().lower() == "x":
+ sample_data[str(sample)] = float(val)
+ return sample_data
+
+
+def sample_for_trait_lists(corr_results, target_dataset,
+ this_trait, this_dataset, start_vars):
+ """interface function for correlation on top results"""
+
+ sample_data = process_samples(
+ start_vars, this_dataset.group.samplelist)
+ target_dataset.get_trait_data(list(sample_data.keys()))
+ # should filter target traits from here
+ _corr_results = corr_results
+
+ this_trait = retrieve_sample_data(this_trait, this_dataset)
+
+ this_trait_data = {
+ "trait_sample_data": sample_data,
+ "trait_id": start_vars["trait_id"]
+ }
+ results = map_shared_keys_to_values(
+ target_dataset.samplelist, target_dataset.trait_data)
+ correlation_results = compute_all_sample_correlation(corr_method="pearson",
+ this_trait=this_trait_data,
+ target_dataset=results)
+
+ return correlation_results
+
+
+def tissue_for_trait_lists(corr_results, this_dataset, this_trait):
+ """interface function for doing tissue corr_results on trait_list"""
+ trait_lists = dict([(list(corr_result)[0], True)
+ for corr_result in corr_results])
+ # trait_lists = {list(corr_results)[0]: 1 for corr_result in corr_results}
+ traits_symbol_dict = this_dataset.retrieve_genes("Symbol")
+ traits_symbol_dict = dict({trait_name: symbol for (
+ trait_name, symbol) in traits_symbol_dict.items() if trait_lists.get(trait_name)})
+ primary_tissue_data, target_tissue_data = get_tissue_correlation_input(
+ this_trait, traits_symbol_dict)
+ corr_results = compute_tissue_correlation(
+ primary_tissue_dict=primary_tissue_data,
+ target_tissues_data=target_tissue_data,
+ corr_method="pearson")
+ return corr_results
+
+
+def lit_for_trait_list(corr_results, this_dataset, this_trait):
+ (this_trait_geneid, geneid_dict, species) = do_lit_correlation(
+ this_trait, this_dataset)
+
+ # trait_lists = {list(corr_results)[0]: 1 for corr_result in corr_results}
+ trait_lists = dict([(list(corr_result)[0], True)
+ for corr_result in corr_results])
+
+ geneid_dict = {trait_name: geneid for (trait_name, geneid) in geneid_dict.items() if
+ trait_lists.get(trait_name)}
+
+ conn, _cursor_object = database_connector()
+
+ with conn:
+
+ correlation_results = compute_all_lit_correlation(
+ conn=conn, trait_lists=list(geneid_dict.items()),
+ species=species, gene_id=this_trait_geneid)
+
+ return correlation_results
+
+
+def compute_correlation(start_vars, method="pearson"):
+ """compute correlation for to call gn3 api"""
+ # pylint: disable-msg=too-many-locals
+
+ corr_type = start_vars['corr_type']
+
+ (this_dataset, this_trait, target_dataset,
+ sample_data) = create_target_this_trait(start_vars)
+
+ method = start_vars['corr_sample_method']
+ corr_return_results = int(start_vars.get("corr_return_results", 100))
+ corr_input_data = {}
+
+ if corr_type == "sample":
+
+ sample_data = process_samples(
+ start_vars, this_dataset.group.samplelist)
+ target_dataset.get_trait_data(list(sample_data.keys()))
+ this_trait = retrieve_sample_data(this_trait, this_dataset)
+ this_trait_data = {
+ "trait_sample_data": sample_data,
+ "trait_id": start_vars["trait_id"]
+ }
+ results = map_shared_keys_to_values(
+ target_dataset.samplelist, target_dataset.trait_data)
+ correlation_results = compute_all_sample_correlation(corr_method=method,
+ this_trait=this_trait_data,
+ target_dataset=results)
+
+ # do tissue correaltion
+
+ # code to be use later
+
+ # tissue_result = tissue_for_trait_lists(
+ # correlation_results, this_dataset, this_trait)
+ # # lit spoils the party so slow
+ # lit_result = lit_for_trait_list(
+ # correlation_results, this_dataset, this_trait)
+
+
+ elif corr_type == "tissue":
+ trait_symbol_dict = this_dataset.retrieve_genes("Symbol")
+ primary_tissue_data, target_tissue_data = get_tissue_correlation_input(
+ this_trait, trait_symbol_dict)
+
+ corr_input_data = {
+ "primary_tissue": primary_tissue_data,
+ "target_tissues_dict": target_tissue_data
+ }
+ correlation_results = compute_tissue_correlation(
+ primary_tissue_dict=corr_input_data["primary_tissue"],
+ target_tissues_data=corr_input_data[
+ "target_tissues_dict"],
+ corr_method=method
+
+ )
+
+ elif corr_type == "lit":
+ (this_trait_geneid, geneid_dict, species) = do_lit_correlation(
+ this_trait, this_dataset)
+
+ conn, _cursor_object = database_connector()
+ with conn:
+ correlation_results = compute_all_lit_correlation(
+ conn=conn, trait_lists=list(geneid_dict.items()),
+ species=species, gene_id=this_trait_geneid)
+
+ return correlation_results[0:corr_return_results]
+
+
+def do_lit_correlation(this_trait, this_dataset):
+ """function for fetching lit inputs"""
+ geneid_dict = this_dataset.retrieve_genes("GeneId")
+ species = this_dataset.group.species.lower()
+ trait_geneid = this_trait.geneid
+ return (trait_geneid, geneid_dict, species)
+
+
+def get_tissue_correlation_input(this_trait, trait_symbol_dict):
+ """Gets tissue expression values for the primary trait and target tissues values"""
+ primary_trait_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values(
+ symbol_list=[this_trait.symbol])
+ if this_trait.symbol.lower() in primary_trait_tissue_vals_dict:
+ primary_trait_tissue_values = primary_trait_tissue_vals_dict[this_trait.symbol.lower(
+ )]
+ corr_result_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values(
+ symbol_list=list(trait_symbol_dict.values()))
+ primary_tissue_data = {
+ "this_id": this_trait.name,
+ "tissue_values": primary_trait_tissue_values
+
+ }
+ target_tissue_data = {
+ "trait_symbol_dict": trait_symbol_dict,
+ "symbol_tissue_vals_dict": corr_result_tissue_vals_dict
+ }
+ return (primary_tissue_data, target_tissue_data)
+ return None
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index 9b0b6118..7fc9f955 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -96,6 +96,7 @@ class CorrelationResults:
self.p_range_lower = get_float(start_vars, 'p_range_lower', -1.0)
self.p_range_upper = get_float(start_vars, 'p_range_upper', 1.0)
+
if ('loc_chr' in start_vars
and 'min_loc_mb' in start_vars
and 'max_loc_mb' in start_vars):
@@ -200,6 +201,7 @@ class CorrelationResults:
if chr_info.name == trait_object.chr:
chr_as_int = order_id
+
if (float(self.correlation_data[trait][0]) >= self.p_range_lower
and float(self.correlation_data[trait][0]) <= self.p_range_upper):
diff --git a/wqflask/wqflask/templates/test_correlation_page.html b/wqflask/wqflask/templates/test_correlation_page.html
new file mode 100644
index 00000000..037e9735
--- /dev/null
+++ b/wqflask/wqflask/templates/test_correlation_page.html
@@ -0,0 +1,159 @@
+{% extends "base.html" %}
+{% block title %}Correlation Results{% endblock %}
+{% block css %}
+ <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" />
+ <link rel="stylesheet" type="text/css" href="{{ url_for('js', filename='DataTablesExtensions/buttonsBootstrap/css/buttons.bootstrap.css') }}" />
+ <link rel="stylesheet" type="text/css" href="{{ url_for('js', filename='DataTablesExtensions/buttonStyles/css/buttons.dataTables.min.css') }}">
+ <link rel="stylesheet" type="text/css" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.1/css/all.min.css">
+ <link rel="stylesheet" type="text/css" href="/static/new/css/trait_list.css" />
+ <link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" />
+
+ <style type="text/css">
+ .td-styles{
+ height: 40px;
+ text-align: center;
+ }
+ .trait_col {
+ font-weight:bolder;
+ text-align: center;
+ color:#036ffc;
+ /*font-size: 1.1em;*/
+ }
+ table th {
+ font-weight: bolder;
+ text-transform: uppercase;
+ }
+ .correlation-title {
+ padding:25px 10px;
+ }
+ .correlation-title h3 span {
+ font-weight: bolder;
+ }
+ .header-toggle-vis {
+ padding:10px 5px;
+ }
+ .header-toggle-vis button {
+ border-radius: 5px;
+
+ }
+ </style>
+{% endblock %}
+
+{% block content %}
+
+<div class="correlation-title">
+ <h3>Correlation Results for <span>Dataset_name</span> against <span><a href="">trait_name</a></span> for the top <span>all</span> Results</h3>
+</div>
+<div class="header-toggle-vis">
+ <h4 style="font-weight: bolder;padding: 5px 3px;">Toggle Columns</h4>
+ <button class="toggle-vis" data-column="1">Index</button>
+ <button class="toggle-vis" data-column="2">Trait Name</button>
+ <button class="toggle-vis" data-column="3">Sample r</button>
+ <button class="toggle-vis" data-column="4">Sample P(r)</button>
+ <button class="toggle-vis" data-column="5">Num overlap</button>
+</div>
+ <table id="example" class="display" width="100%">
+ <thead>
+ <tr >
+ <th></th>
+ <th>index</th>
+ <th>trait_name</th>
+ <th>Sample r</th>
+ <th>Sample r(p)</th>
+ <th>N</th>
+ <th>Tissue r</th>
+ <th>Tissue r(p)</th>
+ <th>Lit r</th>
+ </tr>
+ </thead>
+ </table>
+
+{% endblock %}
+
+{% block js %}
+<script type="text/javascript" src="{{ url_for('js', filename='js_alt/md5.min.js') }}"></script>
+<script type="text/javascript" src="/static/new/javascript/search_results.js"></script>
+
+<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/underscore.min.js') }}"></script>
+<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='jszip/jszip.min.js') }}"></script>
+<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/underscore.min.js') }}"></script>
+<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script>
+<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/buttons/js/dataTables.buttons.min.js') }}"></script>
+<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/buttons/js/buttons.html5.min.js') }}"></script>
+<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/plugins/sorting/natural.js') }}"></script>
+<script language="javascript" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.1/js/all.min.js"></script>
+<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/scroller/js/dataTables.scroller.min.js') }}"></script>
+<script type="text/javascript">
+ console.log("running this script")
+ let correlationResults = {{correlation_results|safe}}
+ // document.querySelector(".content").innerHTML =correlationResults
+ // parse the data
+ let counter = 0;
+ let corr_type = "tissue";
+ correlationResults =correlationResults.map((trait_object)=>{
+ let trait_name = Object.keys(trait_object)[0]
+
+ let new_dict = {
+ "index":counter,
+ "trait_name":trait_name,
+ ...trait_object[trait_name]
+ }
+ counter++;
+ return new_dict;
+ })
+
+console.log(correlationResults)
+
+</script>
+
+<script type="text/javascript">
+ $(document).ready(function() {
+ let table = $('#example').DataTable( {
+ "data": correlationResults,
+ "columns": [
+ {"data":corr_type=="sample"?null:"fd","width":"25px"},
+ { "data": "index","width":"120px","title":"Index" },
+ { "data": "trait_name","title":"TraitName"},
+ { "data": "corr_coeffient","defaultContent": "--"},
+ { "data": "p_value","defaultContent":"--"},
+ { "data": "num_overlap","defaultContent":"--"},
+ {"data":"tissue_corr","defaultContent":"--","title":"Tissue r"},
+ {"data":"tissue_p_val","defaultContent":"--","title":"Tissue r(p)"},
+ {"data":"lit_corr","defaultContent":"--","title":"Lit rho"}
+ ],
+ "columnDefs": [
+ {
+ targets:0,
+ data:null,
+ defaultContent: '',
+ orderable: false,
+ className: 'select-checkbox',
+ "render":(data,type,row)=>{
+ return `<input type="checkbox" class="checkbox trait_checkbox" value="other">`
+ }
+
+ },
+ {className:"trait_col",targets:2},
+ {className: "td-styles", targets: "_all"},
+ {
+ "targets":2,
+ "render":(data,type,row)=>{
+ let urlLink = "/show_trait?trait_id=1453207_at&dataset=HC_M2_0606_P"
+ let traitLink = `<a href=${urlLink}>${data}</a>`
+ return traitLink
+ },
+ }
+
+ ]
+ } );
+
+ $(":button.toggle-vis").on("click",function(e){
+ e.preventDefault()
+ let column = table.column($(this).attr("data-column"));
+ column.visible(!column.visible())
+ console.log($(this).attr("data-column"))
+ })
+} );
+</script>
+
+{% endblock %} \ No newline at end of file
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 276d3019..317c5f63 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -47,6 +47,7 @@ from wqflask.marker_regression import run_mapping
from wqflask.marker_regression import display_mapping_results
from wqflask.network_graph import network_graph
from wqflask.correlation import show_corr_results
+from wqflask.correlation.correlation_gn3_api import compute_correlation
from wqflask.correlation_matrix import show_corr_matrix
from wqflask.correlation import corr_scatter_plot
from wqflask.wgcna import wgcna_analysis
@@ -947,8 +948,14 @@ def network_graph_page():
def corr_compute_page():
logger.info("In corr_compute, request.form is:", pf(request.form))
logger.info(request.url)
- template_vars = show_corr_results.CorrelationResults(request.form)
- return render_template("correlation_page.html", **template_vars.__dict__)
+ # template_vars = show_corr_results.CorrelationResults(request.form)
+ # return render_template("correlation_page.html", **template_vars.__dict__)
+
+ # to test the new correlation api uncomment these lines
+
+ correlation_results = compute_correlation(request.form)
+ # print(">>>>Time taken by this endpoint",time.time()-initial_time)
+ return render_template("test_correlation_page.html",correlation_results=correlation_results)
@app.route("/corr_matrix", methods=('POST',))
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-23 01:48:56 +0000