diff options
| -rw-r--r-- | doc/heatmap-generation.org | 34 | ||||
| -rw-r--r-- | doc/images/gn2_header_collections.png | bin | 0 -> 7890 bytes | |||
| -rw-r--r-- | doc/images/heatmap_form.png | bin | 0 -> 9363 bytes | |||
| -rw-r--r-- | doc/images/heatmap_with_hover_tools.png | bin | 0 -> 42578 bytes | |||
| -rw-r--r-- | etc/default_settings.py | 1 | ||||
| -rw-r--r-- | wqflask/tests/unit/wqflask/wgcna/__init__.py | 0 | ||||
| -rw-r--r-- | wqflask/tests/unit/wqflask/wgcna/test_wgcna.py | 50 | ||||
| -rw-r--r-- | wqflask/wqflask/collect.py | 7 | ||||
| -rw-r--r-- | wqflask/wqflask/marker_regression/run_mapping.py | 2 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/collections/view.html | 101 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/test_wgcna_results.html | 158 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/tool_buttons.html | 4 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/wgcna_setup.html | 198 | ||||
| -rw-r--r-- | wqflask/wqflask/views.py | 11 | ||||
| -rw-r--r-- | wqflask/wqflask/wgcna/gn3_wgcna.py | 102 |
15 files changed, 617 insertions, 51 deletions
diff --git a/doc/heatmap-generation.org b/doc/heatmap-generation.org new file mode 100644 index 00000000..a697c70b --- /dev/null +++ b/doc/heatmap-generation.org @@ -0,0 +1,34 @@ +#+STARTUP: inlineimages +#+TITLE: Heatmap Generation +#+AUTHOR: Muriithi Frederick Muriuki + +* Generating Heatmaps + +Like a lot of other features, the heatmap generation requires an existing collection. If none exists, see [[][Creating a new collection]] for how to create a new collection. + +Once you have a collection, you can navigate to the collections page by clicking on the "Collections" link in the header + + +[[./images/gn2_header_collections.png]] + +From that page, pick the collection that you want to work with by clicking on its name on the collections table. + +That takes you to that collection's page, where you can select the data that you want to use to generate the heatmap. + +** Selecting Orientation + +Once you have selected the data, select the orientation of the heatmap you want generated. You do this by selecting either *"vertical"* or *"horizontal"* in the heatmaps form: + +[[./images/heatmap_form.png]] + +Once you have selected the orientation, click on the "Generate Heatmap" button as in the image above. + +The heatmap generation might take a while, but once it is done, an image shows up above the data table. + +** Downloading the PNG copy of the Heatmap + +Once the heatmap image is shown, hovering over it, displays some tools to interact with the image. + +To download, hover over the heatmap image, and click on the "Download plot as png" icon as shown. + +[[./images/heatmap_with_hover_tools.png]] diff --git a/doc/images/gn2_header_collections.png b/doc/images/gn2_header_collections.png new file mode 100644 index 00000000..ac23f9c1 --- /dev/null +++ b/doc/images/gn2_header_collections.png Binary files differdiff --git a/doc/images/heatmap_form.png b/doc/images/heatmap_form.png new file mode 100644 index 00000000..163fbb60 --- /dev/null +++ b/doc/images/heatmap_form.png Binary files differdiff --git a/doc/images/heatmap_with_hover_tools.png b/doc/images/heatmap_with_hover_tools.png new file mode 100644 index 00000000..4ab79f99 --- /dev/null +++ b/doc/images/heatmap_with_hover_tools.png Binary files differdiff --git a/etc/default_settings.py b/etc/default_settings.py index a194b10e..023aa53b 100644 --- a/etc/default_settings.py +++ b/etc/default_settings.py @@ -25,7 +25,6 @@ import os import sys GN_VERSION = open("../etc/VERSION", "r").read() -GN_SERVER_URL = "http://localhost:8880/" # REST API server # ---- MySQL diff --git a/wqflask/tests/unit/wqflask/wgcna/__init__.py b/wqflask/tests/unit/wqflask/wgcna/__init__.py new file mode 100644 index 00000000..e69de29b --- /dev/null +++ b/wqflask/tests/unit/wqflask/wgcna/__init__.py diff --git a/wqflask/tests/unit/wqflask/wgcna/test_wgcna.py b/wqflask/tests/unit/wqflask/wgcna/test_wgcna.py new file mode 100644 index 00000000..8e947e2f --- /dev/null +++ b/wqflask/tests/unit/wqflask/wgcna/test_wgcna.py @@ -0,0 +1,50 @@ + +"""module contains for processing gn3 wgcna data""" +from unittest import TestCase + +from wqflask.wgcna.gn3_wgcna import process_wgcna_data + + +class DataProcessingTests(TestCase): + """class contains data processing tests""" + + def test_data_processing(self): + """test for parsing data for datatable""" + output = { + "input": { + "sample_names": ["BXD1", "BXD2", "BXD3", "BXD4", "BXD5", "BXD6"], + + }, + "output": { + "ModEigens": { + "MEturquoise": [ + 0.0646677768085351, + 0.137200224277058, + 0.63451113720732, + -0.544002665501479, + -0.489487590361863, + 0.197111117570427 + ], + "MEgrey": [ + 0.213, + 0.214, + 0.3141, + -0.545, + -0.423, + 0.156, + ] + }}} + + row_data = [['BXD1', 0.065, 0.213], + ['BXD2', 0.137, 0.214], + ['BXD3', 0.635, 0.314], + ['BXD4', -0.544, -0.545], + ['BXD5', -0.489, -0.423], + ['BXD6', 0.197, 0.156]] + + expected_results = { + "col_names": ["sample_names", "MEturquoise", "MEgrey"], + "mod_dataset": row_data + } + + self.assertEqual(process_wgcna_data(output), expected_results) diff --git a/wqflask/wqflask/collect.py b/wqflask/wqflask/collect.py index 01274ba9..3475ae5d 100644 --- a/wqflask/wqflask/collect.py +++ b/wqflask/wqflask/collect.py @@ -12,6 +12,7 @@ from flask import flash from wqflask import app from utility import hmac from utility.formatting import numify +from utility.tools import GN_SERVER_URL from utility.redis_tools import get_redis_conn from base.trait import create_trait @@ -218,8 +219,10 @@ def view_collection(): json_version.append(jsonable(trait_ob)) - collection_info = dict(trait_obs=trait_obs, - uc=uc) + collection_info = dict( + trait_obs=trait_obs, + uc=uc, + heatmap_data_url=f"{GN_SERVER_URL}api/heatmaps/clustered") if "json" in params: return json.dumps(json_version) diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py index 80094057..769b9240 100644 --- a/wqflask/wqflask/marker_regression/run_mapping.py +++ b/wqflask/wqflask/marker_regression/run_mapping.py @@ -230,7 +230,7 @@ class RunMapping: self.perm_strata = get_perm_strata( self.this_trait, primary_samples, self.categorical_vars, self.samples) - self.score_type = "LOD" + self.score_type = "-logP" self.control_marker = start_vars['control_marker'] self.do_control = start_vars['do_control'] if 'mapmethod_rqtl_geno' in start_vars: diff --git a/wqflask/wqflask/templates/collections/view.html b/wqflask/wqflask/templates/collections/view.html index a3090bcf..0ded66a6 100644 --- a/wqflask/wqflask/templates/collections/view.html +++ b/wqflask/wqflask/templates/collections/view.html @@ -36,6 +36,28 @@ <div> <br /> + <form id="heatmaps_form"> + <fieldset> + <legend>Heatmap Orientation</legend> + <label for="heatmap-orient-vertical">Vertical</label> + <input id="heatmap-orient-vertical" + type="radio" + name="vertical" + value="true" /> + <label for="heatmap-orient-horizontal">Horizontal</label> + <input id="heatmap-orient-horizontal" + type="radio" + name="vertical" + value="false" /> + </fieldset> + <button id="clustered-heatmap" + class="btn btn-primary" + data-url="{{heatmap_data_url}}" + title="Generate heatmap from this collection"> + Generate Heatmap + </button> + </form> + <div class="collection-table-options"> <form id="export_form" method="POST" action="/export_traits_csv"> <button class="btn btn-default" id="select_all" type="button"><span class="glyphicon glyphicon-ok"></span> Select All</button> @@ -52,6 +74,8 @@ <button id="delete" class="btn btn-danger submit_special" data-url="/collections/delete" type="button" title="Delete this collection" > Delete Collection</button> </form> </div> + <div id="clustered-heatmap-image-area"> + </div> <div style="margin-top: 10px; margin-bottom: 5px;"> <b>Show/Hide Columns:</b> </div> @@ -139,6 +163,8 @@ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/buttons/js/buttons.colVis.min.js') }}"></script> <script type="text/javascript" src="/static/new/javascript/search_results.js"></script> + <script type="text/javascript" src="{{ url_for('js', filename='plotly/plotly.min.js') }}"></script> + <script language="javascript" type="text/javascript"> $(document).ready( function () { @@ -247,6 +273,81 @@ $("#make_default").on("click", function(){ make_default(); }); + + $("#heatmaps_form").submit(function(e) { + e.preventDefault(); + }); + + function clear_heatmap_area() { + area = document.getElementById("clustered-heatmap-image-area"); + area.querySelectorAll("*").forEach(function(child) { + child.remove(); + }); + } + + function generate_progress_indicator() { + count = 0; + default_message = "Computing" + return function() { + message = default_message; + if(count >= 10) { + count = 0; + } + for(i = 0; i < count; i++) { + message = message + " ."; + } + clear_heatmap_area(); + $("#clustered-heatmap-image-area").append( + '<div class="alert alert-info"' + + ' style="font-weigh: bold; font-size: 150%;">' + + message + '</div>'); + count = count + 1; + }; + } + + function display_clustered_heatmap(heatmap_data) { + clear_heatmap_area(); + image_area = document.getElementById("clustered-heatmap-image-area") + Plotly.newPlot(image_area, heatmap_data) + } + + function process_clustered_heatmap_error(xhr, status, error) { + clear_heatmap_area() + $("#clustered-heatmap-image-area").append( + $( + '<div class="alert alert-danger">ERROR: ' + + xhr.responseJSON.message + + '</div>')); + } + + $("#clustered-heatmap").on("click", function() { + clear_heatmap_area(); + intv = window.setInterval(generate_progress_indicator(), 300); + vert_element = document.getElementById("heatmap-orient-vertical"); + vert_true = vert_element == null ? false : vert_element.checked; + heatmap_url = $(this).attr("data-url") + traits = $(".trait_checkbox:checked").map(function() { + return this.value + }).get(); + $.ajax({ + type: "POST", + url: heatmap_url, + contentType: "application/json", + data: JSON.stringify({ + "traits_names": traits, + "vertical": vert_true + }), + dataType: "JSON", + success: function(data, status, xhr) { + window.clearInterval(intv); + display_clustered_heatmap(data); + }, + error: function(xhr, status, error) { + window.clearInterval(intv); + process_clustered_heatmap_error(xhr, status, error); + } + }); + }); }); </script> diff --git a/wqflask/wqflask/templates/test_wgcna_results.html b/wqflask/wqflask/templates/test_wgcna_results.html new file mode 100644 index 00000000..1dddd393 --- /dev/null +++ b/wqflask/wqflask/templates/test_wgcna_results.html @@ -0,0 +1,158 @@ +{% extends "base.html" %} +{% block title %}WCGNA results{% endblock %} +{% block content %} +<!-- Start of body --> + +<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/xterm/3.14.5/xterm.min.css" integrity="sha512-iLYuqv+v/P4u9erpk+KM83Ioe/l7SEmr7wB6g+Kg1qmEit8EShDKnKtLHlv2QXUp7GGJhmqDI+1PhJYLTsfb8w==" crossorigin="anonymous" referrerpolicy="no-referrer" /> + +<link rel="stylesheet" href="https://cdn.datatables.net/1.11.3/css/jquery.dataTables.min.css"> + + +<style type="text/css"> + + +.container { + min-height: 100vh; + width: 100vw; + padding: 20px; + +} + +.grid_container { + + + width: 80vw; + margin: auto; + padding: 20px; + + + display: grid; + grid-template-columns: repeat(7, 1fr); + /*grid-gap: 5px;*/ + border: 1px solid black; + grid-column-gap: 20px; + +} + +.control_sft_column { + text-align: center; +} + +.grid_container div:not(:last-child) { + border-right: 1px solid #000; +} + +.grid_container .control_sft_column h3 { + font-weight: bold; + font-size: 18px; +} + +.control_net_colors { + + display: flex; + flex-wrap: wrap; + justify-content: space-between; + align-items: center; + text-align: center; +} + + +.control_mod_eigens { + display: grid; + grid-template-columns: repeat(2, 200px); +} + +.control-image{ + display: block; + margin-left: auto; + margin-right: auto; + width: 80vw; +} +</style> +<div class="container"> + <div> + <div > + <h2 style="text-align:center">Soft Thresholds </h2> + <div class="grid_container"> + + {% for key, value in results["data"]["output"]["soft_threshold"].items()%} + <div class="control_sft_column"> + <h3>{{key}}</h3> + {% for val in value %} + <p>{{val|round(3)}}</p> + {% endfor %} + </div> + {% endfor %} + </div> + </div> + + <div> + + {% if image["image_generated"] %} + <div > + <img class="control-image" src="data:image/jpeg;base64,{{ image['image_data']| safe }}"> + </div> + + {% endif %} +<!-- <div > + <img class="control-image" src="data:image/jpeg;base64,{{ results['data']['output']['image_data2']| safe }}"> + </div> --> + </div> + + <div> + <h2 style="text-align:center;"> Module eigen genes </h2> + <table id="eigens" class="display" width="80vw"></table> + </div> + + <div> + <h2 style="text-align:center;">Phenotype modules </h2> + + <table id="phenos" class="display" width="40vw" ></table> + </div> + </div> +</div> + +{% endblock %} + +{% block js %} + +<script src="https://cdnjs.cloudflare.com/ajax/libs/xterm/3.14.5/xterm.min.js"></script> + +<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.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/scroller/js/dataTables.scroller.min.js') }}"></script> + + +<script type="text/javascript"> + + +let results = {{results|safe}} + +let phenoModules = results["data"]["output"]["net_colors"] +let phenotypes = Object.keys(phenoModules) +let phenoMods = Object.values(phenoModules) + +let {col_names,mod_dataset} = {{data|safe}} + $('#eigens').DataTable( { + data: mod_dataset, + columns: col_names.map((name)=>{ + return { + title:name + } + }) + } ); + $('#phenos').DataTable( { + data:phenotypes.map((phenoName,idx)=>{ + return [phenoName,phenoMods[idx]] + }), + columns: [{ + title:"Phenotypes" + }, + { + title: "Modules" + }] + } ); + + +</script> +{% endblock %} \ No newline at end of file diff --git a/wqflask/wqflask/templates/tool_buttons.html b/wqflask/wqflask/templates/tool_buttons.html index 3f9d8211..3ee5be19 100644 --- a/wqflask/wqflask/templates/tool_buttons.html +++ b/wqflask/wqflask/templates/tool_buttons.html @@ -18,13 +18,13 @@ BNW </button> -<!-- <button id="wgcna_setup" class="btn btn-primary submit_special" data-url="/wgcna_setup" title="WGCNA Analysis" > +<button id="wgcna_setup" class="btn btn-primary submit_special" data-url="/wgcna_setup" title="WGCNA Analysis" > WGCNA </button> <button id="ctl_setup" class="btn btn-primary submit_special" data-url="/ctl_setup" title="CTL Analysis" > CTL Maps -</button> --> +</button> <button id="heatmap" class="btn btn-primary submit_special" data-url="/heatmap" title="Heatmap" > MultiMap diff --git a/wqflask/wqflask/templates/wgcna_setup.html b/wqflask/wqflask/templates/wgcna_setup.html index c5461497..86d9fa10 100644 --- a/wqflask/wqflask/templates/wgcna_setup.html +++ b/wqflask/wqflask/templates/wgcna_setup.html @@ -1,49 +1,161 @@ {% extends "base.html" %} {% block title %}WCGNA analysis{% endblock %} +{% block content %} +<!-- Start of body --> +<style type="text/css"> + +#terminal { + margin-top: 10px; +} + +</style> +<link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/xterm@4.14.1/css/xterm.css"> -{% block content %} <!-- Start of body --> -<h1> WGCNA analysis parameters</h1> <div class="container"> - {% if request.form['trait_list'].split(",")|length < 4 %} - <div class="alert alert-danger" role="alert"> - <span class="glyphicon glyphicon-exclamation-sign" aria-hidden="true"></span> - <span class="sr-only">Error:</span> - <h2>Too few phenotypes as input</h2> - Please make sure you select enough phenotypes / genes to perform WGCNA. Your collection needs to contain at least 4 different phenotypes. You provided {{request.form['trait_list'].split(',')|length}} phenotypes as input. - </div> - {% else %} - <form action="/wgcna_results" method="post" class="form-horizontal"> - <input type="hidden" name="trait_list" id="trait_list" value= "{{request.form['trait_list']}}"> - <div class="form-group"> - <label for="SoftThresholds"> Soft threshold: </label> - <div class="col-sm-10"> - <input type="text" class="form-inline" name="SoftThresholds" id="SoftThresholds" value="1,2,3,4,5,6,7,8,9"> - </div> - </div> - <div class="form-group"> - <label for="MinModuleSize"> Minimum module size: </label> - <div class="col-sm-10"> - <input type="text" class="form-inline" name="MinModuleSize" id="MinModuleSize" value="30"> - </div> - </div> - <div class="form-group"> - <label for="TOMtype"> TOMtype: </label> - <div class="col-sm-10"> - <input type="text" class="form-inline" name="TOMtype" id="TOMtype" value="unsigned"> - </div> - </div> - <div class="form-group"> - <label for="mergeCutHeight"> mergeCutHeight: </label> - <div class="col-sm-10"> - <input type="text" class="form-inline" name="mergeCutHeight" id="mergeCutHeight" value="0.25"> - </div> + <div class="col-md-5"> + <h1 class="mx-3 my-2 "> WGCNA analysis parameters</h1> + {% if request.form['trait_list'].split(",")|length < 4 %} <div class="alert alert-danger" role="alert"> + <span class="glyphicon glyphicon-exclamation-sign" aria-hidden="true"></span> + <span class="sr-only">Error:</span> + <h2>Too few phenotypes as input</h2> + Please make sure you select enough phenotypes / genes to perform WGCNA. Your collection needs to contain at least 4 different phenotypes. You provided {{request.form['trait_list'].split(',')|length}} phenotypes as input. </div> - <div class="form-group"> - <div class="col-sm-10"> - <input type="submit" class="btn btn-primary" value="Run WGCNA using these settings" /> - </div> - </div> - </form> - {% endif %} + {% else %} + <form class="col-md-12" action="/wgcna_results" method="post" class="form-horizontal" id="wgcna_form"> + <input type="hidden" name="trait_list" id="trait_list" value="{{request.form['trait_list']}}"> + <div class="form-group row "> + <label for="SoftThresholds" class="col-md-3 col-form-label col-form-label-sm">Soft threshhold</label> + <div class="col-md-9"> + <input type="text" class="form-control form-control-md" value="1,2,3,4,5,6,7,8,9" id="SoftThresholds" name="SoftThresholds"> + </div> + </div> + <div class="form-group row "> + <label for="MinModuleSize" class="col-md-3 col-form-label col-form-label-sm">Minimum module size:</label> + <div class="col-md-9"> + <input type="text" class="form-control form-control-md" id="MinModuleSize" value="30" name="MinModuleSize"> + </div> + </div> + + <div class="form-group row"> + <label for="TOMtype" class="col-md-3 col-form-label col-form-label-sm">TOMtype:</label> + <div class="col-md-9"> + <select class="form-control" id="TOMtype" name="TOMtype"> + <option value="unsigned">unsigned</option> + <option value="signed">signed</option> + </select> + </div> + + </div> + <div class="form-group row "> + <label for="mergeCutHeight" class="col-md-3 col-form-label col-form-label-sm">mergeCutHeight:</label> + <div class="col-md-9"> + <input type="text" class="form-control form-control-md" id="mergeCutHeight" value="0.25" name="mergeCutHeight"> + </div> + </div> + + <div class="form-group row"> + <label for="corType" class="col-md-3 col-form-label col-form-label-sm">corType:</label> + <div class="col-md-9"> + <select class="form-control col-md-9" id="corType" name="corType"> + <option value="pearson">pearson</option> + <option value="bicor">bicor</option> + </select> + </div> + + </div> + <div class="form-group"> + <div class="text-center"> + <input type="submit" class="btn btn-primary" value="Run WGCNA using these settings" /> + </div> + </div> + + + + </form> + {% endif %} </div> -{% endblock %} +<div class="col-md-7"> + <div id="terminal" class="mt-2"> + </div> +</div> +</div> + +<script src="https://cdn.socket.io/4.2.0/socket.io.min.js" integrity="sha384-PiBR5S00EtOj2Lto9Uu81cmoyZqR57XcOna1oAuVuIEjzj0wpqDVfD0JA9eXlRsj" crossorigin="anonymous"></script> + +<script src="https://cdn.jsdelivr.net/npm/xterm@4.14.1/lib/xterm.min.js"></script> + +<script src="https://cdn.jsdelivr.net/npm/xterm-addon-attach@0.6.0/lib/xterm-addon-attach.min.js"></script> + + +<script src="https://cdn.jsdelivr.net/npm/xterm-addon-fit@0.5.0/lib/xterm-addon-fit.min.js"></script> + <script src="https://code.jquery.com/jquery-3.5.1.js" + integrity="sha256-QWo7LDvxbWT2tbbQ97B53yJnYU3WhH/C8ycbRAkjPDc=" + crossorigin="anonymous"></script> +<script> +// document.addEventListener('DOMContentLoaded', function() { +let term = new Terminal({ + cursorBlink: true, + lineHeight: 1.3, + scrollback: true, + macOptionIsMeta: true +}); + +let termDebugs = { + general: "Computation process to be displayed here....", + success: "Computation in process ......", + fail: "Too few phenotypes as input must be >=4" +} + +const fitAddon = new FitAddon.FitAddon() +term.loadAddon(fitAddon) + +term.open(document.getElementById('terminal')); +term.setOption('theme', { + background: '#300a24' +}); +term.writeln(termDebugs.general) + +wgcnaForm = document.querySelector("#wgcna_form") + +const socket = io("http://127.0.0.1:8081") //issue gn3 private +const attachAddon = new AttachAddon.AttachAddon(socket); + +term.loadAddon(attachAddon); + +fitAddon.fit() +term.onData((data) => { + term.write(data) +}) + + +if (wgcnaForm) { +} else { + term.writeln(termDebugs.fail) +} + +socket.on("connect", () => { + $("#wgcna_form").append(`<input type="hidden" name="socket_id" value=${socket.id}>`); +}) + +socket.on("output", ({ + data +}) => { + term.writeln(data) +}) + +$(document).on('submit', '#wgcna_form', function(e) { + term.writeln(termDebugs.success) + + e.preventDefault(); + var form = $(this); + $.ajax({ + type: 'POST', + url: '/wgcna_results', + data: form.serialize(), + success: function(data) { + document.write(data) + } + }) +}); +</script> +{% endblock %} \ No newline at end of file diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index 5067ca0e..b0da1f21 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -40,8 +40,8 @@ from gn3.db.phenotypes import Probeset from gn3.db.phenotypes import Publication from gn3.db.phenotypes import PublishXRef from gn3.db.phenotypes import probeset_mapping -from gn3.db.traits import get_trait_csv_sample_data -from gn3.db.traits import update_sample_data +# from gn3.db.traits import get_trait_csv_sample_data +# from gn3.db.traits import update_sample_data from flask import current_app @@ -79,6 +79,7 @@ from wqflask.correlation_matrix import show_corr_matrix from wqflask.correlation import corr_scatter_plot # from wqflask.wgcna import wgcna_analysis # from wqflask.ctl import ctl_analysis +from wqflask.wgcna.gn3_wgcna import run_wgcna from wqflask.snp_browser import snp_browser from wqflask.search_results import SearchResultPage from wqflask.export_traits import export_search_results_csv @@ -376,6 +377,12 @@ def wcgna_setup(): return render_template("wgcna_setup.html", **request.form) +@app.route("/wgcna_results", methods=('POST',)) +def wcgna_results(): + """call the gn3 api to get wgcna response data""" + results = run_wgcna(dict(request.form)) + return render_template("test_wgcna_results.html", **results) + @app.route("/ctl_setup", methods=('POST',)) def ctl_setup(): # We are going to get additional user input for the analysis diff --git a/wqflask/wqflask/wgcna/gn3_wgcna.py b/wqflask/wqflask/wgcna/gn3_wgcna.py new file mode 100644 index 00000000..c4cc2e7f --- /dev/null +++ b/wqflask/wqflask/wgcna/gn3_wgcna.py @@ -0,0 +1,102 @@ +"""module contains code to consume gn3-wgcna api +and process data to be rendered by datatables +""" + +import requests +from types import SimpleNamespace +from utility.helper_functions import get_trait_db_obs + + +def fetch_trait_data(requestform): + """fetch trait data""" + db_obj = SimpleNamespace() + get_trait_db_obs(db_obj, + [trait.strip() + for trait in requestform['trait_list'].split(',')]) + + return process_dataset(db_obj.trait_list) + + +def process_dataset(trait_list): + """process datasets and strains""" + + input_data = {} + traits = [] + strains = [] + + # xtodo unique traits and strains + + for trait in trait_list: + traits.append(trait[0].name) + + input_data[trait[0].name] = {} + for strain in trait[0].data: + strains.append(strain) + input_data[trait[0].name][strain] = trait[0].data[strain].value + # "sample_names": list(set(strains)), + # "trait_names": form_traits, + # "trait_sample_data": form_strains, + + return { + "input": input_data, + "trait_names": traits, + "sample_names": strains + } + + +def process_wgcna_data(response): + """function for processing modeigene genes + for create row data for datataba""" + mod_eigens = response["output"]["ModEigens"] + + sample_names = response["input"]["sample_names"] + + mod_dataset = [[sample] for sample in sample_names] + + for _, mod_values in mod_eigens.items(): + for (index, _sample) in enumerate(sample_names): + mod_dataset[index].append(round(mod_values[index], 3)) + + return { + "col_names": ["sample_names", *mod_eigens.keys()], + "mod_dataset": mod_dataset + } + + +def process_image(response): + """function to process image check if byte string is empty""" + image_data = response["output"]["image_data"] + return ({ + "image_generated": True, + "image_data": image_data + } if image_data else { + "image_generated": False + }) + + +def run_wgcna(form_data): + """function to run wgcna""" + + GN3_URL = "http://127.0.0.1:8081" + + wgcna_api = f"{GN3_URL}/api/wgcna/run_wgcna" + + # parse form data + + trait_dataset = fetch_trait_data(form_data) + form_data["minModuleSize"] = int(form_data["MinModuleSize"]) + + response = requests.post(wgcna_api, json={ + "sample_names": list(set(trait_dataset["sample_names"])), + "trait_names": trait_dataset["trait_names"], + "trait_sample_data": list(trait_dataset["input"].values()), + **form_data + + } + ).json() + + return { + "results": response, + "data": process_wgcna_data(response["data"]), + "image": process_image(response["data"]) + } |
