gsMap 1.67__py3-none-any.whl → 1.71__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (32) hide show
  1. gsMap/{GNN_VAE → GNN}/__init__.py +0 -0
  2. gsMap/{GNN_VAE → GNN}/adjacency_matrix.py +75 -75
  3. gsMap/{GNN_VAE → GNN}/model.py +89 -89
  4. gsMap/{GNN_VAE → GNN}/train.py +88 -86
  5. gsMap/__init__.py +5 -5
  6. gsMap/__main__.py +2 -2
  7. gsMap/cauchy_combination_test.py +141 -141
  8. gsMap/config.py +805 -803
  9. gsMap/diagnosis.py +273 -273
  10. gsMap/find_latent_representation.py +133 -145
  11. gsMap/format_sumstats.py +407 -407
  12. gsMap/generate_ldscore.py +618 -618
  13. gsMap/latent_to_gene.py +234 -234
  14. gsMap/main.py +31 -31
  15. gsMap/report.py +160 -160
  16. gsMap/run_all_mode.py +194 -194
  17. gsMap/setup.py +0 -0
  18. gsMap/spatial_ldsc_multiple_sumstats.py +380 -380
  19. gsMap/templates/report_template.html +198 -198
  20. gsMap/utils/__init__.py +0 -0
  21. gsMap/utils/generate_r2_matrix.py +735 -735
  22. gsMap/utils/jackknife.py +514 -514
  23. gsMap/utils/make_annotations.py +518 -518
  24. gsMap/utils/manhattan_plot.py +639 -639
  25. gsMap/utils/regression_read.py +294 -294
  26. gsMap/visualize.py +198 -198
  27. {gsmap-1.67.dist-info → gsmap-1.71.dist-info}/LICENSE +21 -21
  28. {gsmap-1.67.dist-info → gsmap-1.71.dist-info}/METADATA +28 -22
  29. gsmap-1.71.dist-info/RECORD +31 -0
  30. gsmap-1.67.dist-info/RECORD +0 -31
  31. {gsmap-1.67.dist-info → gsmap-1.71.dist-info}/WHEEL +0 -0
  32. {gsmap-1.67.dist-info → gsmap-1.71.dist-info}/entry_points.txt +0 -0
gsMap/templates/report_template.html CHANGED
@@ -1,198 +1,198 @@
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- <!DOCTYPE html>
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- <html lang="en">
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- <head>
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- <meta charset="UTF-8">
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- <title>{{ title }}</title>
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- <meta name="viewport" content="width=device-width, initial-scale=1">
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- <!-- Bootstrap CSS -->
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- <link href="https://cdn.jsdelivr.net/npm/bootstrap@5.3.0/dist/css/bootstrap.min.css" rel="stylesheet">
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- <!-- Custom Styles -->
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- <style>
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- body {
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- padding: 20px;
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- font-family: 'Helvetica Neue', Helvetica, Arial, sans-serif;
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- }
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- .plot-container {
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- margin-bottom: 50px;
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- }
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- .section-description {
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- color: #6c757d;
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- font-size: 0.95rem;
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- margin-bottom: 20px;
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- }
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- .scrollable-table {
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- max-height: 400px;
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- overflow-y: auto;
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- }
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- .table thead th {
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- position: sticky;
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- top: 0;
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- background-color: #f8f9fa;
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- }
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- img {
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- max-width: 100%;
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- height: auto;
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- border: 1px solid #dee2e6;
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- border-radius: 5px;
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- }
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- .gene-select-label {
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- font-weight: bold;
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- margin-bottom: 10px;
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- }
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- .collapse-toggle {
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- cursor: pointer;
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- color: #0d6efd;
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- text-decoration: underline;
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- }
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- </style>
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- </head>
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- <body>
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- <div class="container-fluid">
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- <h1 class="mb-4">{{ title }}</h1>
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-
53
- <!-- Genetic Spatial Mapping Plot -->
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- <div class="plot-container">
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- <h2>Genetic Spatial Mapping Plot</h2>
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- <p class="section-description">This plot shows the spatial genetic mapping results across different tissues.</p>
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- <div class="border rounded p-3">
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- {{ genetic_mapping_plot|safe }}
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- </div>
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- </div>
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-
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- <!-- Cauchy Combination Result Table -->
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- <div class="plot-container">
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- <h2>Cauchy Combination Result</h2>
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- <p class="section-description">This table presents the results of the Cauchy combination test, summarizing the genetic associations.</p>
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- <div class="scrollable-table">
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- <table class="table table-hover table-bordered">
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- <thead class="table-light">
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- <tr>
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- <th>Annotation</th>
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- <th>P Cauchy</th>
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- <th>P Median</th>
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- </tr>
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- </thead>
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- <tbody>
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- {% for row in cauchy_table %}
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- <tr>
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- <td>{{ row.annotation }}</td>
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- <td>{{ "%.4e"|format(row.p_cauchy) }}</td>
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- <td>{{ "%.4e"|format(row.p_median) }}</td>
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- </tr>
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- {% endfor %}
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- </tbody>
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- </table>
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- </div>
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- </div>
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-
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- <!-- Manhattan Plot -->
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- <div class="plot-container">
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- <h2>Diagnosis Manhattan Plot</h2>
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- <p class="section-description">The Manhattan plot shows the association of SNPs with the top associated gene across the genome.</p>
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- <div class="border rounded p-3">
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- {{ manhattan_plot|safe }}
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- </div>
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- </div>
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-
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- <!-- Gene Expression and GSS Distribution -->
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- <div class="plot-container">
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- <h2>Gene Expression and GSS Distribution</h2>
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- <p class="section-description">Select a gene to view its expression distribution and gene specificity score (GSS).</p>
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- <label for="geneSelect" class="gene-select-label">Select a gene:</label>
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- <select id="geneSelect" class="form-select mb-4">
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- {% for gene in gene_plots %}
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- <option value="{{ gene.name }}">{{ gene.name }}</option>
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- {% endfor %}
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- </select>
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- <div id="genePlots" class="row">
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- <div class="col-md-6 mb-4">
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- <h5>Expression Distribution</h5>
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- <img src="{{ gene_plots[0].expression_plot }}" alt="{{ gene_plots[0].name }} Expression Distribution" id="expressionPlotImg" class="img-fluid">
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- </div>
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- <div class="col-md-6 mb-4">
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- <h5>Gene Specificity Score (GSS)</h5>
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- <img src="{{ gene_plots[0].gss_plot }}" alt="{{ gene_plots[0].name }} GSS Distribution" id="gssPlotImg" class="img-fluid">
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- </div>
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- </div>
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- </div>
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-
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- <!-- Gene Diagnostic Info Table -->
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- <div class="plot-container">
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- <h2>Top 50 Gene Diagnostic Info</h2>
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- <p class="section-description">This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.</p>
123
- <div class="scrollable-table">
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- <table class="table table-hover table-bordered">
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- <thead class="table-light">
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- <tr>
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- <th>Gene</th>
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- <th>Annotation</th>
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- <th>Median GSS</th>
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- <th>PCC</th>
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- </tr>
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- </thead>
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- <tbody>
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- {% for row in gene_diagnostic_info %}
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- <tr>
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- <td>{{ row.Gene }}</td>
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- <td>{{ row.Annotation }}</td>
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- <td>{{ "%.4f"|format(row.Median_GSS) }}</td>
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- <td>{{ "%.4f"|format(row.PCC) }}</td>
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- </tr>
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- {% endfor %}
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- </tbody>
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- </table>
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- </div>
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- </div>
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-
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- <!-- Running Info (collapsible) -->
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- <div class="plot-container">
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- <h2>Running Info</h2>
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- <p class="section-description">Click to view detailed run information and parameters.</p>
151
- <p class="collapse-toggle" data-bs-toggle="collapse" href="#runningInfo" role="button" aria-expanded="false" aria-controls="runningInfo">
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- Show/Hide Running Info
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- </p>
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- <div class="collapse" id="runningInfo">
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- <div class="card card-body">
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- <p><strong>gsMap Version:</strong> {{ gsmap_version }}</p>
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- <p><strong>Parameters:</strong></p>
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- <ul class="mb-0">
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- {% for key, value in parameters.items() %}
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- <li><strong>{{ key }}:</strong> {{ value }}</li>
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- {% endfor %}
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- </ul>
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- </div>
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- </div>
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- </div>
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- </div>
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-
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- <!-- JavaScript for Gene Plots -->
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- <script src="https://cdn.jsdelivr.net/npm/bootstrap@5.3.0/dist/js/bootstrap.bundle.min.js"></script>
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- <script>
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- (function() {
172
- const geneSelect = document.getElementById('geneSelect');
173
- const expressionPlotImg = document.getElementById('expressionPlotImg');
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- const gssPlotImg = document.getElementById('gssPlotImg');
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-
176
- const genePlots = {
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- {% for gene in gene_plots %}
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- "{{ gene.name }}": {
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- expression_plot: "{{ gene.expression_plot }}",
180
- gss_plot: "{{ gene.gss_plot }}"
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- }{% if not loop.last %},{% endif %}
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- {% endfor %}
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- };
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-
185
- geneSelect.addEventListener('change', function() {
186
- const selectedGene = this.value;
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- const selectedGenePlots = genePlots[selectedGene];
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-
189
- // Update images
190
- expressionPlotImg.src = selectedGenePlots.expression_plot;
191
- expressionPlotImg.alt = `${selectedGene} Expression Distribution`;
192
- gssPlotImg.src = selectedGenePlots.gss_plot;
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- gssPlotImg.alt = `${selectedGene} GSS Distribution`;
194
- });
195
- })();
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- </script>
197
- </body>
198
- </html>
1
+ <!DOCTYPE html>
2
+ <html lang="en">
3
+ <head>
4
+ <meta charset="UTF-8">
5
+ <title>{{ title }}</title>
6
+ <meta name="viewport" content="width=device-width, initial-scale=1">
7
+ <!-- Bootstrap CSS -->
8
+ <link href="https://cdn.jsdelivr.net/npm/bootstrap@5.3.0/dist/css/bootstrap.min.css" rel="stylesheet">
9
+ <!-- Custom Styles -->
10
+ <style>
11
+ body {
12
+ padding: 20px;
13
+ font-family: 'Helvetica Neue', Helvetica, Arial, sans-serif;
14
+ }
15
+ .plot-container {
16
+ margin-bottom: 50px;
17
+ }
18
+ .section-description {
19
+ color: #6c757d;
20
+ font-size: 0.95rem;
21
+ margin-bottom: 20px;
22
+ }
23
+ .scrollable-table {
24
+ max-height: 400px;
25
+ overflow-y: auto;
26
+ }
27
+ .table thead th {
28
+ position: sticky;
29
+ top: 0;
30
+ background-color: #f8f9fa;
31
+ }
32
+ img {
33
+ max-width: 100%;
34
+ height: auto;
35
+ border: 1px solid #dee2e6;
36
+ border-radius: 5px;
37
+ }
38
+ .gene-select-label {
39
+ font-weight: bold;
40
+ margin-bottom: 10px;
41
+ }
42
+ .collapse-toggle {
43
+ cursor: pointer;
44
+ color: #0d6efd;
45
+ text-decoration: underline;
46
+ }
47
+ </style>
48
+ </head>
49
+ <body>
50
+ <div class="container-fluid">
51
+ <h1 class="mb-4">{{ title }}</h1>
52
+
53
+ <!-- Genetic Spatial Mapping Plot -->
54
+ <div class="plot-container">
55
+ <h2>Genetic Spatial Mapping Plot</h2>
56
+ <p class="section-description">This plot shows the spatial genetic mapping results across different tissues.</p>
57
+ <div class="border rounded p-3">
58
+ {{ genetic_mapping_plot|safe }}
59
+ </div>
60
+ </div>
61
+
62
+ <!-- Cauchy Combination Result Table -->
63
+ <div class="plot-container">
64
+ <h2>Cauchy Combination Result</h2>
65
+ <p class="section-description">This table presents the results of the Cauchy combination test, summarizing the genetic associations.</p>
66
+ <div class="scrollable-table">
67
+ <table class="table table-hover table-bordered">
68
+ <thead class="table-light">
69
+ <tr>
70
+ <th>Annotation</th>
71
+ <th>P Cauchy</th>
72
+ <th>P Median</th>
73
+ </tr>
74
+ </thead>
75
+ <tbody>
76
+ {% for row in cauchy_table %}
77
+ <tr>
78
+ <td>{{ row.annotation }}</td>
79
+ <td>{{ "%.4e"|format(row.p_cauchy) }}</td>
80
+ <td>{{ "%.4e"|format(row.p_median) }}</td>
81
+ </tr>
82
+ {% endfor %}
83
+ </tbody>
84
+ </table>
85
+ </div>
86
+ </div>
87
+
88
+ <!-- Manhattan Plot -->
89
+ <div class="plot-container">
90
+ <h2>Diagnosis Manhattan Plot</h2>
91
+ <p class="section-description">The Manhattan plot shows the association of SNPs with the top associated gene across the genome.</p>
92
+ <div class="border rounded p-3">
93
+ {{ manhattan_plot|safe }}
94
+ </div>
95
+ </div>
96
+
97
+ <!-- Gene Expression and GSS Distribution -->
98
+ <div class="plot-container">
99
+ <h2>Gene Expression and GSS Distribution</h2>
100
+ <p class="section-description">Select a gene to view its expression distribution and gene specificity score (GSS).</p>
101
+ <label for="geneSelect" class="gene-select-label">Select a gene:</label>
102
+ <select id="geneSelect" class="form-select mb-4">
103
+ {% for gene in gene_plots %}
104
+ <option value="{{ gene.name }}">{{ gene.name }}</option>
105
+ {% endfor %}
106
+ </select>
107
+ <div id="genePlots" class="row">
108
+ <div class="col-md-6 mb-4">
109
+ <h5>Expression Distribution</h5>
110
+ <img src="{{ gene_plots[0].expression_plot }}" alt="{{ gene_plots[0].name }} Expression Distribution" id="expressionPlotImg" class="img-fluid">
111
+ </div>
112
+ <div class="col-md-6 mb-4">
113
+ <h5>Gene Specificity Score (GSS)</h5>
114
+ <img src="{{ gene_plots[0].gss_plot }}" alt="{{ gene_plots[0].name }} GSS Distribution" id="gssPlotImg" class="img-fluid">
115
+ </div>
116
+ </div>
117
+ </div>
118
+
119
+ <!-- Gene Diagnostic Info Table -->
120
+ <div class="plot-container">
121
+ <h2>Top 50 Gene Diagnostic Info</h2>
122
+ <p class="section-description">This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.</p>
123
+ <div class="scrollable-table">
124
+ <table class="table table-hover table-bordered">
125
+ <thead class="table-light">
126
+ <tr>
127
+ <th>Gene</th>
128
+ <th>Annotation</th>
129
+ <th>Median GSS</th>
130
+ <th>PCC</th>
131
+ </tr>
132
+ </thead>
133
+ <tbody>
134
+ {% for row in gene_diagnostic_info %}
135
+ <tr>
136
+ <td>{{ row.Gene }}</td>
137
+ <td>{{ row.Annotation }}</td>
138
+ <td>{{ "%.4f"|format(row.Median_GSS) }}</td>
139
+ <td>{{ "%.4f"|format(row.PCC) }}</td>
140
+ </tr>
141
+ {% endfor %}
142
+ </tbody>
143
+ </table>
144
+ </div>
145
+ </div>
146
+
147
+ <!-- Running Info (collapsible) -->
148
+ <div class="plot-container">
149
+ <h2>Running Info</h2>
150
+ <p class="section-description">Click to view detailed run information and parameters.</p>
151
+ <p class="collapse-toggle" data-bs-toggle="collapse" href="#runningInfo" role="button" aria-expanded="false" aria-controls="runningInfo">
152
+ Show/Hide Running Info
153
+ </p>
154
+ <div class="collapse" id="runningInfo">
155
+ <div class="card card-body">
156
+ <p><strong>gsMap Version:</strong> {{ gsmap_version }}</p>
157
+ <p><strong>Parameters:</strong></p>
158
+ <ul class="mb-0">
159
+ {% for key, value in parameters.items() %}
160
+ <li><strong>{{ key }}:</strong> {{ value }}</li>
161
+ {% endfor %}
162
+ </ul>
163
+ </div>
164
+ </div>
165
+ </div>
166
+ </div>
167
+
168
+ <!-- JavaScript for Gene Plots -->
169
+ <script src="https://cdn.jsdelivr.net/npm/bootstrap@5.3.0/dist/js/bootstrap.bundle.min.js"></script>
170
+ <script>
171
+ (function() {
172
+ const geneSelect = document.getElementById('geneSelect');
173
+ const expressionPlotImg = document.getElementById('expressionPlotImg');
174
+ const gssPlotImg = document.getElementById('gssPlotImg');
175
+
176
+ const genePlots = {
177
+ {% for gene in gene_plots %}
178
+ "{{ gene.name }}": {
179
+ expression_plot: "{{ gene.expression_plot }}",
180
+ gss_plot: "{{ gene.gss_plot }}"
181
+ }{% if not loop.last %},{% endif %}
182
+ {% endfor %}
183
+ };
184
+
185
+ geneSelect.addEventListener('change', function() {
186
+ const selectedGene = this.value;
187
+ const selectedGenePlots = genePlots[selectedGene];
188
+
189
+ // Update images
190
+ expressionPlotImg.src = selectedGenePlots.expression_plot;
191
+ expressionPlotImg.alt = `${selectedGene} Expression Distribution`;
192
+ gssPlotImg.src = selectedGenePlots.gss_plot;
193
+ gssPlotImg.alt = `${selectedGene} GSS Distribution`;
194
+ });
195
+ })();
196
+ </script>
197
+ </body>
198
+ </html>
gsMap/utils/__init__.py CHANGED
File without changes