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G3-521 gene counts for setting threshold #31

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Dec 9, 2024
Merged

G3-521 gene counts for setting threshold #31

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2 changes: 1 addition & 1 deletion pyproject.toml
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
[tool.poetry]
name = "geneweaver-legacy"
version = "1.5.3"
version = "1.5.4"
description = ""
authors = ["Alexander Berger <[email protected]>"]
readme = "README.md"
Expand Down
41 changes: 36 additions & 5 deletions src/application.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1972,6 +1972,7 @@ def render_set_threshold(gs_id):
threshold_type = geneset.threshold_type
threshold = str(geneset.threshold)
thresh = threshold.split(',')
threshold_gene_counts = None

minVal = None
maxVal = None
Expand All @@ -1986,9 +1987,6 @@ def render_set_threshold(gs_id):
if gsv_values is not None:
for k in gsv_values:
k_first_value = list(k.values())[0]
# maxVal = maxVal if maxVal is not None and float(k_first_value) < maxVal else float(k_first_value)
# minVal = minVal if minVal is not None and float(k_first_value) > minVal else float(k_first_value)

if maxVal is not None:
maxVal = float(k_first_value) if float(k_first_value) > maxVal else maxVal
else:
Expand All @@ -1999,8 +1997,15 @@ def render_set_threshold(gs_id):
else:
minVal = float(k_first_value)

# minVal = float(k_first_value) if float(k_first_value) < minVal else minVal
g_values.append(float(k_first_value))


# if Threshold type is 1 or 2 (p-value or q-value) then calculate gene counts for each threshold
curr_gene_count = 0;
if threshold_type == 1 or threshold_type == 2:
threshold_gene_counts = calc_genes_count_in_threshold(gsv_values, thresh)
curr_gene_count = curr_gene_count if thresh[0] == 'None' else threshold_gene_counts[float(thresh[0])]

score_types = {
1: "p-value",
2: "q-value",
Expand All @@ -2013,7 +2018,33 @@ def render_set_threshold(gs_id):
user_id=user_id, view=view, is_bimodal=is_bimodal,
threshold=thresh, threshold_type=threshold_type,
minVal=minVal, maxVal=maxVal,
scoreType=score_types[threshold_type], gsv_values=g_values)
scoreType=score_types[threshold_type], gsv_values=g_values,
threshold_gene_counts=threshold_gene_counts, curr_gene_count=curr_gene_count)

def calc_genes_count_in_threshold(gsv_values, curr_thresh) -> dict:
""" Calculate the number of genes that fall below a given threshold
for score types 1 and 2 (p-value and q-value)

:param gsv_values: list of gene set values
:return: dictionary of gene counts for each threshold
"""
threshold_gene_counts = {}
thresholds = [0.05, 0.01, 0.001, 0.0001]

# Add the current threshold to the list
if curr_thresh[0] != 'None' and float(curr_thresh[0]) not in thresholds:
thresholds.append(float(curr_thresh[0]))

for threshold in thresholds:
threshold_gene_counts[threshold] = 0
if gsv_values is not None:
for gsv_value in gsv_values:
value = list(gsv_value.values())[0]
if float(value) < threshold:
threshold_gene_counts[threshold] += 1

return threshold_gene_counts



@app.route('/setthreshold-legacy/<int:gs_id>')
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93 changes: 65 additions & 28 deletions src/templates/viewThreshold_new.html
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Original file line number Diff line number Diff line change
Expand Up @@ -21,27 +21,37 @@ <h2 class="panel-title"><strong>Set GeneSet Threshold</strong></h2>
<div class="panel-body">
{% set threshold_symbol = 'p' if threshold_type == 1 else 'q' %}
{% if is_bimodal == 'False' %}
<div class="row">
{% if threshold_type == 4 or threshold_type == 5 %}
{% set threshold_low = threshold[0] if threshold[0] != 'None' else minVal %}
{% set threshold_high = threshold[1] if threshold[1] != '0' else maxVal %}
{% set threshold_name = 'a correlation' if threshold_type == 4 else 'an effect' %}
<div><p><strong>Current Threshold Values:
</strong> {{ threshold[0] }} <i class="fa fa-arrows-h"></i>
{% if threshold[1] == '0' %}
None
{% else %}
{{ threshold[1] }}
{% endif %}
</p>
{% if gsv_values|length == 0 %}
<div class="row">
<div class="alert bg-gray-light">
This GeneSet does not contain any geneset values.
Set threshold cannot be performed.
</div>
</div>
{% else %}
<div><p><strong>Current Threshold Values:
</strong> {{ threshold_symbol }} < {{ threshold[0] }}
</p>
<div class="row">
{% if threshold_type == 4 or threshold_type == 5 %}
{% set threshold_low = threshold[0] if threshold[0] != 'None' else minVal %}
{% set threshold_high = threshold[1] if threshold[1] != '0' else maxVal %}
{% set threshold_name = 'a correlation' if threshold_type == 4 else 'an effect' %}
<div><p><strong>Current Threshold Values:
</strong> {{ threshold[0] }} <i class="fa fa-arrows-h"></i>
{% if threshold[1] == '0' %}
None
{% else %}
{{ threshold[1] }}
{% endif %}
</p>
</div>
{% else %}
<div><p><strong>Current Threshold Values:
</strong> {{ threshold_symbol }} < {{ threshold[0] }} ( genes count: {{ curr_gene_count }} )
</p>
</div>
{% endif %}

</div>
{% endif %}
</div>
{% else %}
<div class="row">
<div class="alert bg-gray-light">
Expand All @@ -53,7 +63,7 @@ <h2 class="panel-title"><strong>Set GeneSet Threshold</strong></h2>
<hr>
<div class="row">
<div class="col-md-9" style="margin-bottom: 1rem;">
{% if view is defined and is_bimodal == 'False' %}
{% if view is defined and is_bimodal == 'False' and gsv_values|length > 0%}
{% if threshold_type == 4 or threshold_type == 5 %}
<div class="row">
<div class="input-group">
Expand All @@ -68,24 +78,37 @@ <h2 class="panel-title"><strong>Set GeneSet Threshold</strong></h2>
</div>
<div class="row">
<div class="col-md-12" style="margin-bottom: 1rem;">
<div id="myHisPlot" style="width:100%; height:500px;"></div>
<p>** Use Box Select tool to set a threshold range on the histogram, or enter values in the input fields. </p>
<p>* Selected threshold range in red color</p>
<div class="row">
<div class="col-md-12" style="margin-top: 2rem; margin-bottom: 1rem;">
<p id="selectedGeneCount"></p>
</div>
</div>
<div class="row">
<div class="col-md-12" style="margin-bottom: 1rem;">
<div id="myHisPlot" style="width:100%; height:500px;"></div>
</div>
</div>
<div class="row">
<div class="col-md-12" style="margin-bottom: 1rem;">
<p>** Use Box Select tool to set a threshold range on the histogram, or enter values in the input fields. </p>
<p>* Selected threshold range in red color</p>
</div>
</div>
</div>
</div>
{% else %}
<div class="row">
<button type="button" class="btn btn-block btn-default setThresh" id="setThresh05" value="0.05">
Save as <code> {{ threshold_symbol }} < 0.05 </code>
Save as <code> {{ threshold_symbol }} < 0.05 </code> ( genes count: {{ threshold_gene_counts[0.05]}} )
</button>
<button type="button" class="btn btn-block btn-default setThresh" id="setThresh01" value="0.01">
Save as <code> {{ threshold_symbol }} < 0.01 </code>
Save as <code> {{ threshold_symbol }} < 0.01 </code> ( genes count: {{ threshold_gene_counts[0.01]}} )
</button>
<button type="button" class="btn btn-block btn-default setThresh" id="setThresh001" value="0.001">
Save as <code> {{ threshold_symbol }} < 0.001 </code>
Save as <code> {{ threshold_symbol }} < 0.001 </code> ( genes count:{{ threshold_gene_counts[0.001]}} )
</button>
<button type="button" class="btn btn-block btn-default setThresh" id="setThresh0001" value="0.0001">
Save as <code> {{ threshold_symbol }} < 0.0001 </code>
Save as <code> {{ threshold_symbol }} < 0.0001 </code> ( genes count: {{ threshold_gene_counts[0.0001]}} )
</button>

<hr>
Expand Down Expand Up @@ -200,6 +223,13 @@ <h2 class="panel-title"><strong>Set GeneSet Threshold</strong></h2>
}
}
});
//update gene count display
displaySelectedGeneCount(indices.length);
}

//Display selected gene count
function displaySelectedGeneCount(count) {
document.getElementById('selectedGeneCount').innerHTML = '<b>Number of Genes in Selected Threshold:</b> ' + count;
}

// Set properties for Plotly histogram
Expand Down Expand Up @@ -256,6 +286,12 @@ <h2 class="panel-title"><strong>Set GeneSet Threshold</strong></h2>

// Callback function for selected points using Box Select tool
myPlot.on('plotly_selected', function(data) {
var geneCount = 0;
for (var i = 0; i < data.points.length; i++) {
geneCount = data.points[i].pointIndices.length + geneCount;
}
//update gene count display
displaySelectedGeneCount(geneCount);

if (data !== undefined) {
threshold_min.value = data.range.x[0];
Expand Down Expand Up @@ -286,7 +322,10 @@ <h2 class="panel-title"><strong>Set GeneSet Threshold</strong></h2>
}
setSelectPoints(myPlot, selected_x)
} else {
//Do nothing -- index for values will not be found in histogram data
//Index for values will not be found in histogram data
//update histogram selection and gene count display to 0
setSelectPoints(myPlot, [])
displaySelectedGeneCount(0);
console.log('Threshold values not found in histogram', 'index_min:', index_min, 'index_max:', index_max);
}
}
Expand All @@ -308,8 +347,6 @@ <h2 class="panel-title"><strong>Set GeneSet Threshold</strong></h2>

{% endif %}



</div>

{% endif %}
Expand Down
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