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-rw-r--r--wqflask/wqflask/marker_regression/display_mapping_results.py26
-rw-r--r--wqflask/wqflask/marker_regression/run_mapping.py7
-rw-r--r--wqflask/wqflask/templates/mapping_results.html47
-rw-r--r--wqflask/wqflask/templates/search_result_page.html4
-rw-r--r--wqflask/wqflask/views.py2
5 files changed, 74 insertions, 12 deletions
diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py
index 3f6de2b2..08c2d750 100644
--- a/wqflask/wqflask/marker_regression/display_mapping_results.py
+++ b/wqflask/wqflask/marker_regression/display_mapping_results.py
@@ -74,6 +74,14 @@ DARKVIOLET = ImageColor.getrgb("darkviolet")
MEDIUMPURPLE = ImageColor.getrgb("mediumpurple")
# ---- END: Define common colours ---- #
+# ZS: List of distinct colors for manhattan plot if user selects "varied"
+COLOR_CODES = ["#FF0000", "#00FF00", "#0000FF", "#FFFF00", "#FF00FF", "#00FFFF",
+ "#000000", "#800000", "#008000", "#000080", "#808000", "#800080",
+ "#008080", "#808080", "#C00000", "#00C000", "#0000C0", "#C0C000",
+ "#C000C0", "#00C0C0", "#C0C0C0", "#400000", "#004000", "#000040"]
+
+DISTINCT_COLOR_LIST = [ImageColor.getrgb(color) for color in COLOR_CODES]
+
# ---- FONT FILES ---- #
VERDANA_FILE = "./wqflask/static/fonts/verdana.ttf"
VERDANA_BOLD_FILE = "./wqflask/static/fonts/verdanab.ttf"
@@ -293,6 +301,12 @@ class DisplayMappingResults(object):
self.plotScale = "physic"
self.manhattan_plot = start_vars['manhattan_plot']
+ if self.manhattan_plot:
+ self.color_scheme = "alternating"
+ if 'color_scheme' in start_vars:
+ self.color_scheme = start_vars['color_scheme']
+ if self.color_scheme == "single":
+ self.manhattan_single_color = ImageColor.getrgb("#" + start_vars['manhattan_single_color'])
if 'permCheck' in list(start_vars.keys()):
self.permChecked = start_vars['permCheck']
@@ -2424,10 +2438,16 @@ class DisplayMappingResults(object):
Yc = yZero - qtlresult['lod_score']*LRSHeightThresh/LRS_LOD_Max
if self.manhattan_plot == True:
- if self.selectedChr == -1 and (previous_chr_as_int % 2 == 1):
- point_color = RED
+ if self.color_scheme == "single":
+ point_color = self.manhattan_single_color
+ elif self.color_scheme == "varied":
+ point_color = DISTINCT_COLOR_LIST[previous_chr_as_int]
else:
- point_color = BLUE
+ if self.selectedChr == -1 and (previous_chr_as_int % 2 == 1):
+ point_color = RED
+ else:
+ point_color = BLUE
+
im_drawer.text(
text="5",
xy=(
diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py
index 31d6a67c..c474e0e0 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -138,7 +138,12 @@ class RunMapping(object):
mapping_results_filename = self.dataset.group.name + "_" + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6))
self.mapping_results_path = "{}{}.csv".format(webqtlConfig.GENERATED_IMAGE_DIR, mapping_results_filename)
- if start_vars['manhattan_plot'] == "true":
+ if start_vars['manhattan_plot']:
+ self.color_scheme = "alternating"
+ if "color_scheme" in start_vars:
+ self.color_scheme = start_vars['color_scheme']
+ if self.color_scheme == "single":
+ self.manhattan_single_color = start_vars['manhattan_single_color']
self.manhattan_plot = True
else:
self.manhattan_plot = False
diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html
index 28d93542..9542c29d 100644
--- a/wqflask/wqflask/templates/mapping_results.html
+++ b/wqflask/wqflask/templates/mapping_results.html
@@ -40,6 +40,9 @@
<input type="hidden" name="use_loco" value="{{ use_loco }}">
<input type="hidden" name="selected_chr" value="{{ selectedChr }}">
<input type="hidden" name="manhattan_plot" value="{{ manhattan_plot }}">
+ {% if manhattan_plot == True %}
+ <input type="hidden" name="color_scheme" value="alternating">
+ {% endif %}
<input type="hidden" name="num_perm" value="{{ nperm }}">
<input type="hidden" name="perm_info" value="">
<input type="hidden" name="perm_strata" value="{{ perm_strata }}">
@@ -55,7 +58,7 @@
<input type="hidden" name="wanted_inputs" value="">
<input type="hidden" name="form_url" value="/run_mapping">
- <div class="container">
+ <div class="container" style="min-width: 1400px;">
<div class="col-xs-5">
<h2>Map Viewer: Whole Genome</h2><br>
<b>Population:</b> {{ dataset.group.species|capitalize }} {{ dataset.group.name }}<br>
@@ -77,7 +80,7 @@
<table>
<tr>
<td><b>Chr:&nbsp;</b></td>
- <td>
+ <td style="padding: 5px;">
<select name="chromosomes" size="1">
{% for chr in ChrList %}
<option value="{{ chr[1] }}" {% if (chr[1] + 1) == selectedChr %}selected{% endif %}>{{ chr[0] }}</option>
@@ -87,7 +90,7 @@
</td>
</tr>
<tr>
- <td><b>View:&nbsp;</b></td>
+ <td ><b>View:&nbsp;</b></td>
<td style="padding: 5px;">
<input type="text" name="startMb" size="7" value="{% if startMb != -1 %}{{ startMb }}{% endif %}"> to <input type="text" name="endMb" size="7" value="{% if endMb != -1 %}{{ endMb }}{% endif %}">
</td>
@@ -114,11 +117,31 @@
</tr>
<tr>
<td><b>Width:&nbsp;</b></td>
- <td>
+ <td style="padding: 5px;">
<input type="text" name="graphWidth" value="{% if graphWidth is defined %}{{ graphWidth }}{% else %}1600{% endif %}" size="5"><span style="font-size: 12px;"> pixels (minimum=900)</span>
</td>
</tr>
</table>
+ {% if manhattan_plot == True and selectedChr == -1 %}
+ <table style="margin-top: 10px;">
+ <tr>
+ <td>
+ <b>Manhattan Plot Color Scheme:&nbsp;</b>
+ </td>
+ <td>
+ <select id="color_scheme">
+ <option value="alternating" {% if color_scheme == "alternating" %}selected{% endif %}>Alternating</option>
+ <option value="varied" {% if color_scheme == "varied" %}selected{% endif %}>Varied by Chr</option>
+ <option value="single" {% if color_scheme == "single" %}selected{% endif %}>Single Color</option>
+ </select>
+ </td>
+ <td>
+ <input name="manhattan_single_color" type="hidden" id="point_color" value={% if manhattan_single_color %}{{ manhattan_single_color }}{% else %}"#D9D9D9"{% endif %}>
+ <button style="display: none; margin-left: 5px;" id="point_color_picker" class="jscolor {valueElement: 'point_color'}">Choose Color</button>
+ </td>
+ </tr>
+ </table>
+ {% endif %}
</div>
<div class="col-xs-4" style="padding: 0px;">
{% if (mapping_method == "reaper" or mapping_method == "rqtl_geno") and nperm > 0 %}
@@ -328,6 +351,9 @@
<script type="text/javascript" src="{{ url_for('js', filename='underscore-string/underscore.string.min.js') }}"></script>
<script type="text/javascript" src="{{ url_for('js', filename='d3-tip/d3-tip.js') }}"></script>
<script type="text/javascript" src="/static/new/js_external/plotly-latest.min.js"></script>
+ {% if manhattan_plot == True and selectedChr == -1 %}
+ <script type="text/javascript" src="/static/new/js_external/jscolor.js"></script>
+ {% endif %}
<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="https://cdn.datatables.net/buttons/1.0.0/js/dataTables.buttons.min.js"></script>
@@ -423,7 +449,7 @@
var mapping_input_list = ['temp_uuid', 'trait_id', 'dataset', 'tool_used', 'form_url', 'method', 'transform', 'trimmed_markers', 'selected_chr', 'chromosomes', 'mapping_scale',
'score_type', 'suggestive', 'significant', 'num_perm', 'permCheck', 'perm_output', 'perm_strata', 'categorical_vars', 'num_bootstrap', 'bootCheck', 'bootstrap_results',
- 'LRSCheck', 'covariates', 'maf', 'use_loco', 'manhattan_plot', 'control_marker', 'control_marker_db', 'do_control', 'genofile',
+ 'LRSCheck', 'covariates', 'maf', 'use_loco', 'manhattan_plot', 'color_scheme', 'manhattan_single_color', 'control_marker', 'control_marker_db', 'do_control', 'genofile',
'pair_scan', 'startMb', 'endMb', 'graphWidth', 'lrsMax', 'additiveCheck', 'showSNP', 'showGenes', 'viewLegend', 'haplotypeAnalystCheck',
'mapmethod_rqtl_geno', 'mapmodel_rqtl_geno', 'temp_trait', 'group', 'species', 'reaper_version', 'primary_samples', 'n_samples']
@@ -449,10 +475,21 @@
remap = function() {
$('input[name=selected_chr]').val($('select[name=chromosomes]').val());
+ $('input[name=color_scheme]').val($('select#color_scheme').val());
$('#marker_regression_form').attr('action', '/loading');
return $('#marker_regression_form').submit();
};
+ {% if manhattan_plot == True and selectedChr == -1 %}
+ $('#color_scheme').change(function(){
+ if ($(this).val() == "single"){
+ $('#point_color_picker').show();
+ } else {
+ $('#point_color_picker').hide();
+ }
+ });
+ {% endif %}
+
{% if mapping_method != "gemma" and mapping_method != "plink" %}
$('#download_perm').click(function(){
perm_info_dict = {
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index 8e2b06a4..9a28a78e 100644
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -2,9 +2,9 @@
{% block title %}Search 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('css', filename='fontawesome/css/font-awesome.min.css') }}" />
<link rel="stylesheet" type="text/css" href="{{ url_for('js', filename='DataTablesExtensions/scroller/css/scroller.dataTables.min.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/show_trait.css" />
<link rel="stylesheet" type="text/css" href="static/new/css/trait_list.css" />
{% endblock %}
@@ -440,8 +440,6 @@
'processing': 'Loading...'
}
} );
-
- console.timeEnd("Creating table");
$('.toggle-vis').on( 'click', function (e) {
e.preventDefault();
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 91d0842c..3557a62a 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -697,6 +697,8 @@ def mapping_results_page():
'maf',
'use_loco',
'manhattan_plot',
+ 'color_scheme',
+ 'manhattan_single_color',
'control_marker',
'control_marker_db',
'do_control',
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-26 21:50:05 +0000