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-rwxr-xr-xwqflask/wqflask/correlation_matrix/show_corr_matrix.py51
-rwxr-xr-xwqflask/wqflask/marker_regression/marker_regression.py4
-rwxr-xr-xwqflask/wqflask/static/new/css/corr_matrix.css18
-rw-r--r--wqflask/wqflask/static/new/javascript/chr_lod_chart.js19
-rw-r--r--wqflask/wqflask/static/new/javascript/create_lodchart.js4
-rw-r--r--wqflask/wqflask/static/new/javascript/lod_chart.js13
-rw-r--r--wqflask/wqflask/static/new/javascript/panelutil.js12
-rwxr-xr-xwqflask/wqflask/templates/correlation_matrix.html45
-rwxr-xr-xwqflask/wqflask/templates/marker_regression.html4
-rwxr-xr-xwqflask/wqflask/templates/search_result_page.html4
10 files changed, 137 insertions, 37 deletions
diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
index 2cdd989f..6bc0ef77 100755
--- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
+++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
@@ -95,35 +95,24 @@ class CorrelationMatrix(object):
#self.sample_data[this_trait.name].append('')
self.sample_data.append(this_trait_vals)
+ self.lowest_overlap = 8 #ZS: Variable set to the lowest overlapping samples in order to notify user, or 8, whichever is lower (since 8 is when we want to display warning)
+
self.corr_results = []
- self.corr_results_for_pca = []
+ self.pca_corr_results = []
for trait_db in self.trait_list:
this_trait = trait_db[0]
this_db = trait_db[1]
this_db_samples = this_db.group.samplelist
-
- #for sample in this_db_samples:
- # if sample not in self.samples:
- # self.samples.append(sample)
-
this_sample_data = this_trait.data
- print("this_sample_data", len(this_sample_data))
-
- #for sample in this_sample_data:
- # if sample not in self.all_sample_list:
- # self.all_sample_list.append(sample)
corr_result_row = []
+ pca_corr_result_row = []
is_spearman = False #ZS: To determine if it's above or below the diagonal
for target in self.trait_list:
target_trait = target[0]
target_db = target[1]
target_samples = target_db.group.samplelist
-
- #if this_trait == target_trait and this_db == target_db:
- # corr_result_row.append(1)
- # continue
target_sample_data = target_trait.data
print("target_samples", len(target_samples))
@@ -139,19 +128,26 @@ class CorrelationMatrix(object):
target_vals.append(target_sample_value)
this_trait_vals, target_vals, num_overlap = corr_result_helpers.normalize_values(this_trait_vals, target_vals)
+
+ if num_overlap < self.lowest_overlap:
+ self.lowest_overlap = num_overlap
if num_overlap == 0:
corr_result_row.append([target_trait, 0, num_overlap])
+ pca_corr_result_row.append(0)
else:
+ pearson_r, pearson_p = scipy.stats.pearsonr(this_trait_vals, target_vals)
if is_spearman == False:
- sample_r, sample_p = scipy.stats.pearsonr(this_trait_vals, target_vals)
+ sample_r, sample_p = pearson_r, pearson_p
if sample_r == 1:
is_spearman = True
else:
sample_r, sample_p = scipy.stats.spearmanr(this_trait_vals, target_vals)
corr_result_row.append([target_trait, sample_r, num_overlap])
+ pca_corr_result_row.append(pearson_r)
self.corr_results.append(corr_result_row)
+ self.pca_corr_results.append(pca_corr_result_row)
print("corr_results:", pf(self.corr_results))
@@ -159,8 +155,9 @@ class CorrelationMatrix(object):
for sample in self.all_sample_list:
groups.append(1)
- #pca = self.calculate_pca(self.corr_results, range(len(self.traits)))
+ pca = self.calculate_pca(self.pca_corr_results, range(len(self.traits)))
+ self.loadings_array = self.process_loadings()
self.js_data = dict(traits = [trait.name for trait in self.traits],
groups = groups,
@@ -211,8 +208,24 @@ class CorrelationMatrix(object):
print("eigen:", eigen)
pca = stats.princomp(m, cor = "TRUE")
print("pca:", pca)
- print("loadings:", pca.rx('loadings'))
+ self.loadings = pca.rx('loadings')
+ self.scores = pca.rx('scores')
+ self.scale = pca.rx('scale')
print("scores:", pca.rx('scores'))
print("scale:", pca.rx('scale'))
- return pca \ No newline at end of file
+ return pca
+
+ def process_loadings(self):
+ loadings_array = []
+ loadings_row = []
+ print("before loop:", self.loadings[0])
+ for i in range(len(self.trait_list)):
+ loadings_row = []
+ for j in range(3):
+ position = i + len(self.trait_list)*j
+ loadings_row.append(self.loadings[0][position])
+ loadings_array.append(loadings_row)
+ print("loadings:", loadings_array)
+ return loadings_array
+
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index b33efc1f..dc7ebfcc 100755
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -74,6 +74,7 @@ class MarkerRegression(object):
self.significant = ""
self.pair_scan = False # Initializing this since it is checked in views to determine which template to use
self.score_type = "LRS" #ZS: LRS or LOD
+ self.mapping_scale = "megabase"
self.dataset.group.get_markers()
if self.mapping_method == "gemma":
@@ -86,6 +87,7 @@ class MarkerRegression(object):
results = self.run_rqtl_plink()
elif self.mapping_method == "rqtl_geno":
self.score_type = "LOD"
+ self.mapping_scale = "centimorgan"
if start_vars['num_perm'] == "":
self.num_perm = 0
else:
@@ -136,6 +138,7 @@ class MarkerRegression(object):
data_set = self.dataset.name,
maf = self.maf,
manhattan_plot = self.manhattan_plot,
+ mapping_scale = self.mapping_scale,
qtl_results = self.qtl_results,
)
@@ -191,6 +194,7 @@ class MarkerRegression(object):
data_set = self.dataset.name,
maf = self.maf,
manhattan_plot = self.manhattan_plot,
+ mapping_scale = self.mapping_scale,
chromosomes = chromosome_mb_lengths,
qtl_results = self.qtl_results,
)
diff --git a/wqflask/wqflask/static/new/css/corr_matrix.css b/wqflask/wqflask/static/new/css/corr_matrix.css
index f4838f77..495ca28c 100755
--- a/wqflask/wqflask/static/new/css/corr_matrix.css
+++ b/wqflask/wqflask/static/new/css/corr_matrix.css
@@ -10,3 +10,21 @@
width: 100px;
float: left;
}
+
+.chart {
+
+}
+
+.main text {
+ font: 10px sans-serif;
+}
+
+.axis line, .axis path {
+ shape-rendering: crispEdges;
+ stroke: black;
+ fill: none;
+}
+
+circle {
+ fill: steelblue;
+}
diff --git a/wqflask/wqflask/static/new/javascript/chr_lod_chart.js b/wqflask/wqflask/static/new/javascript/chr_lod_chart.js
index 616a89f6..60878978 100644
--- a/wqflask/wqflask/static/new/javascript/chr_lod_chart.js
+++ b/wqflask/wqflask/static/new/javascript/chr_lod_chart.js
@@ -2,11 +2,12 @@
var Chr_Lod_Chart;
Chr_Lod_Chart = (function() {
- function Chr_Lod_Chart(plot_height, plot_width, chr, manhattanPlot) {
+ function Chr_Lod_Chart(plot_height, plot_width, chr, manhattanPlot, mappingScale) {
this.plot_height = plot_height;
this.plot_width = plot_width;
this.chr = chr;
this.manhattanPlot = manhattanPlot;
+ this.mappingScale = mappingScale;
this.qtl_results = js_data.qtl_results;
console.log("qtl_results are:", this.qtl_results);
console.log("chr is:", this.chr);
@@ -65,8 +66,6 @@ Chr_Lod_Chart = (function() {
} else {
this_chr = result.chr;
}
- console.log("this_chr is:", this_chr);
- console.log("@chr[0] is:", parseInt(this.chr[0]));
if (this_chr > parseInt(this.chr[0])) {
break;
}
@@ -120,7 +119,19 @@ Chr_Lod_Chart = (function() {
};
Chr_Lod_Chart.prototype.create_scales = function() {
- this.x_scale = d3.scale.linear().domain([0, this.chr[1]]).range([this.x_buffer, this.plot_width]);
+ if (this.mappingScale == "centimorgan") {
+ max_pos = 0
+ for (i = 0, len = this.these_results.length; i < len; i++) {
+ marker = this.these_results[i]
+ if (parseFloat(marker['Mb']) > max_pos){
+ max_pos = parseFloat(marker.Mb)
+ }
+ }
+ this.x_scale = d3.scale.linear().domain([0, max_pos]).range([this.x_buffer, this.plot_width]);
+ }
+ else {
+ this.x_scale = d3.scale.linear().domain([0, this.chr[1]]).range([this.x_buffer, this.plot_width]);
+ }
return this.y_scale = d3.scale.linear().domain([0, this.y_max]).range([this.plot_height, this.y_buffer]);
};
diff --git a/wqflask/wqflask/static/new/javascript/create_lodchart.js b/wqflask/wqflask/static/new/javascript/create_lodchart.js
index b8fcf1f8..c756d842 100644
--- a/wqflask/wqflask/static/new/javascript/create_lodchart.js
+++ b/wqflask/wqflask/static/new/javascript/create_lodchart.js
@@ -16,8 +16,8 @@
halfh = h + margin.top + margin.bottom;
totalh = halfh * 2;
totalw = w + margin.left + margin.right;
- //console.log("js_data:", js_data);
- mychart = lodchart().lodvarname("lod.hk").height(h).width(w).margin(margin).ylab(js_data.result_score_type + " score").manhattanPlot(js_data.manhattan_plot);
+ console.log("js_data:", js_data);
+ mychart = lodchart().lodvarname("lod.hk").height(h).width(w).margin(margin).ylab(js_data.result_score_type + " score").mappingScale(js_data.mapping_scale).manhattanPlot(js_data.manhattan_plot);
data = js_data.json_data;
d3.select("div#topchart").datum(data).call(mychart);
chrrect = mychart.chrSelect();
diff --git a/wqflask/wqflask/static/new/javascript/lod_chart.js b/wqflask/wqflask/static/new/javascript/lod_chart.js
index d0d39fe6..014bf59b 100644
--- a/wqflask/wqflask/static/new/javascript/lod_chart.js
+++ b/wqflask/wqflask/static/new/javascript/lod_chart.js
@@ -2,7 +2,7 @@
var lodchart;
lodchart = function() {
- var additive, additive_ylab, additive_ylim, additive_yscale, additive_yticks, additivelinecolor, axispos, chart, chrGap, chrSelect, darkrect, height, lightrect, linewidth, lodcurve, lodlinecolor, lodvarname, manhattanPlot, margin, markerSelect, nyticks, pad4heatmap, pointcolor, pointsAtMarkers, pointsize, pointstroke, rotate_ylab, significantcolor, suggestivecolor, title, titlepos, width, xlab, xscale, ylab, ylim, yscale, yticks;
+ var additive, additive_ylab, additive_ylim, additive_yscale, additive_yticks, additivelinecolor, axispos, chart, chrGap, chrSelect, darkrect, height, lightrect, linewidth, lodcurve, lodlinecolor, lodvarname, manhattanPlot, mappingScale, margin, markerSelect, nyticks, pad4heatmap, pointcolor, pointsAtMarkers, pointsize, pointstroke, rotate_ylab, significantcolor, suggestivecolor, title, titlepos, width, xlab, xscale, ylab, ylim, yscale, yticks;
width = 800;
height = 500;
margin = {
@@ -97,7 +97,7 @@ lodchart = function() {
additive_yticks = additive_yticks != null ? additive_yticks : additive_yscale.ticks(nyticks);
}
reorgLodData(data, lodvarname);
- data = chrscales(data, width, chrGap, margin.left, pad4heatmap);
+ data = chrscales(data, width, chrGap, margin.left, pad4heatmap, mappingScale);
xscale = data.xscale;
chrSelect = g.append("g").attr("class", "chrRect").selectAll("empty").data(data.chrnames).enter().append("rect").attr("id", function(d) {
return "chrrect" + d[0];
@@ -133,7 +133,7 @@ lodchart = function() {
var chr_plot;
$('#topchart').remove();
$('#chart_container').append('<div class="qtlcharts" id="topchart"></div>');
- return chr_plot = new Chr_Lod_Chart(600, 1200, chr_ob, manhattanPlot);
+ return chr_plot = new Chr_Lod_Chart(600, 1200, chr_ob, manhattanPlot, mappingScale);
};
rotate_ylab = rotate_ylab != null ? rotate_ylab : ylab.length > 1;
yaxis = g.append("g").attr("class", "y axis");
@@ -305,6 +305,13 @@ lodchart = function() {
manhattanPlot = value;
return chart;
};
+ chart.mappingScale = function(value) {
+ if (!arguments.length) {
+ return mappingScale;
+ }
+ mappingScale = value;
+ return chart;
+ };
chart.ylim = function(value) {
if (!arguments.length) {
return ylim;
diff --git a/wqflask/wqflask/static/new/javascript/panelutil.js b/wqflask/wqflask/static/new/javascript/panelutil.js
index 113512b4..5a931f7d 100644
--- a/wqflask/wqflask/static/new/javascript/panelutil.js
+++ b/wqflask/wqflask/static/new/javascript/panelutil.js
@@ -105,7 +105,7 @@ reorgLodData = function(data, lodvarname) {
return data;
};
-chrscales = function(data, width, chrGap, leftMargin, pad4heatmap) {
+chrscales = function(data, width, chrGap, leftMargin, pad4heatmap, mappingScale) {
var L, chr, chrEnd, chrLength, chrStart, cur, d, i, maxd, rng, totalChrLength, w, _i, _j, _len, _len1, _ref, _ref1;
chrStart = [];
chrEnd = [];
@@ -156,7 +156,15 @@ chrscales = function(data, width, chrGap, leftMargin, pad4heatmap) {
w = Math.round((width - chrGap * (data.chrnames.length - pad4heatmap)) / totalChrLength * chrLength[i]);
data.chrEnd.push(cur + w);
cur = data.chrEnd[i] + chrGap;
- data.xscale[chr[0]] = d3.scale.linear().domain([chrStart[i], chrEnd[i]]).range([data.chrStart[i], data.chrEnd[i]]);
+
+ if (mappingScale == "centimorgan") {
+ max_pos = d3.max(data.posByChr[chr[0]])
+ console.log("max_pos:", max_pos)
+ data.xscale[chr[0]] = d3.scale.linear().domain([chrStart[i], max_pos]).range([data.chrStart[i], data.chrEnd[i]]);
+ }
+ else {
+ data.xscale[chr[0]] = d3.scale.linear().domain([chrStart[i], chrEnd[i]]).range([data.chrStart[i], data.chrEnd[i]]);
+ }
}
return data;
};
diff --git a/wqflask/wqflask/templates/correlation_matrix.html b/wqflask/wqflask/templates/correlation_matrix.html
index c822b8bc..593c7bea 100755
--- a/wqflask/wqflask/templates/correlation_matrix.html
+++ b/wqflask/wqflask/templates/correlation_matrix.html
@@ -12,7 +12,9 @@
{{ header("Correlation Matrix") }}
-
+{% if lowest_overlap < 8 %}
+<div style="margin: 20px;" >Caution: This matrix of correlations contains some cells with small sample sizes of fewer than 8.</div>
+{% endif %}
<table class="matrix" border="1" cellpadding="5" cellspacing="1" style="margin: 20px;" width="80%">
<tbody>
@@ -42,18 +44,48 @@
</tbody>
</table>
+<br>
+
+<div id="loadings_plot"></div>
+
+<table class="table table-hover table-striped" border="1" id='trait_table' style="margin: 20px;" width="40%">
+ <thead>
+ <tr>
+ <th></th>
+ <th align="right" >Factor 1</th>
+ <th align="right" >Factor 2</th>
+ <th align="right" >Factor 2</th>
<!--
-<div class="container">
- <div id="chart"></div>
-</div>
+ {% for row in loadings_array %}
+ <th>Factor {{ loop.index }}</th>
+ {% endfor %}
-->
+ </tr>
+ </thead>
+ <tbody>
+ {% for row in loadings_array %}
+ {% set row_counter = loop.index-1 %}
+ <tr>
+ <td>
+ <a href="{{ url_for('show_trait_page', trait_id = traits[loop.index-1].name, dataset = traits[loop.index-1].dataset.name) }}">
+ {{ traits[loop.index-1].name }}
+ </a>
+ </td>
+ {% for column in row %}
+ <td><span style="float: right;">{{ '%0.3f' % loadings_array[row_counter][loop.index-1]|float }}</span></td>
+ {% endfor %}
+ </tr>
+ {% endfor %}
+
+ </tbody>
+</table>
{% endblock %}
{% block js %}
<script>
- js_data = {{ js_data | safe }}
+ loadings = {{ loadings_array | safe }}
</script>
<script type="text/javascript" src="http://d3js.org/d3.v3.min.js"></script>
@@ -65,7 +97,6 @@
<script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script>
<script type="text/javascript" src="/static/new/javascript/panelutil.js"></script>
<script language="javascript" type="text/javascript" src="/static/new/js_external/chroma.js"></script>
- <script language="javascript" type="text/javascript" src="/static/new/javascript/corr_matrix.js"></script>
- <script language="javascript" type="text/javascript" src="/static/new/javascript/create_corr_matrix.js"></script>
+ <script language="javascript" type="text/javascript" src="/static/new/javascript/loadings_plot.js"></script>
{% endblock %}
diff --git a/wqflask/wqflask/templates/marker_regression.html b/wqflask/wqflask/templates/marker_regression.html
index 2d0b6256..ad117337 100755
--- a/wqflask/wqflask/templates/marker_regression.html
+++ b/wqflask/wqflask/templates/marker_regression.html
@@ -36,7 +36,11 @@
<th>Index</th>
<th>{{ score_type }}</th>
<th>Chr</th>
+ {% if mapping_scale == "centimorgan" %}
+ <th>cM</th>
+ {% else %}
<th>Mb</th>
+ {% endif %}
<th>Locus</th>
</tr>
</thead>
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index f29b907d..e304be1c 100755
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -15,6 +15,7 @@
<input type="hidden" name="uc_id" id="uc_id" value="{{ uc_id }}">
+ <!-- Need to customize text more for other types of searches -->
<p>We searched <a href="/dbdoc/{{dataset.fullname}}">{{ dataset.fullname }}</a>
to find all records that match
{% for word in search_terms %}
@@ -49,6 +50,8 @@
<input type="text" id="select_top" class="form-control" style="width: 200px; display: inline;" placeholder="Select Top ...">
<br />
<br />
+<!--
+ Removing this until more options are added and work correctly
{% if dataset.type == 'ProbeSet' %}
<button class="btn btn-default" id="open_options">Open Extra Options</button>
<br />
@@ -59,6 +62,7 @@
</div>
<br />
<br />
+-->
{% endif %}
<div id="table_container">
<table class="table table-hover table-striped" id='trait_table' {% if dataset.type == 'Geno' %}width="400px"{% endif %} style="float: left;">