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| author | Alexander Kabui | 2022-03-18 16:58:36 +0300 |
|---|---|---|
| committer | GitHub | 2022-03-18 16:58:36 +0300 |
| commit | 79cfb51939b618ce5afc0278c76b7bb113e14d38 (patch) | |
| tree | 03071ebbae6111be62e7b2a955ac0cf5774f4157 | |
| parent | 205ebb2d9501f431984359b15467cf573803b0a4 (diff) | |
| parent | 33605e355b7335138dd75ef3ffe29d095533933d (diff) | |
| download | genenetwork2-79cfb51939b618ce5afc0278c76b7bb113e14d38.tar.gz | |
Merge pull request #689 from Alexanderlacuna/chore/gn2-enhancements
Chore/gn2 enhancements
4 files changed, 24 insertions, 10 deletions
diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py index 88d62045..cf37b9e9 100644 --- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py +++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py @@ -37,6 +37,7 @@ from gn3.computations.pca import compute_pca from gn3.computations.pca import process_factor_loadings_tdata from gn3.computations.pca import generate_pca_temp_traits from gn3.computations.pca import cache_pca_dataset +from gn3.computations.pca import generate_scree_plot_data class CorrelationMatrix: @@ -169,6 +170,7 @@ class CorrelationMatrix: pca = self.calculate_pca() self.loadings_array = process_factor_loadings_tdata( factor_loadings=self.loadings, traits_num=len(self.trait_list)) + else: self.pca_works = "False" except: @@ -176,6 +178,7 @@ class CorrelationMatrix: self.js_data = dict(traits=[trait.name for trait in self.traits], groups=groups, + scree_data = self.scree_data, cols=list(range(len(self.traits))), rows=list(range(len(self.traits))), samples=self.all_sample_list, @@ -187,6 +190,7 @@ class CorrelationMatrix: self.loadings = pca["components"] self.scores = pca["scores"] + self.pca_obj = pca["pca"] this_group_name = self.trait_list[0][1].group.name temp_dataset = create_dataset( @@ -205,6 +209,13 @@ class CorrelationMatrix: self.pca_trait_ids = list(pca_temp_traits.keys()) + x_coord, y_coord = generate_scree_plot_data( + list(self.pca_obj.explained_variance_ratio_)) + + self.scree_data = { + "x_coord": x_coord, + "y_coord": y_coord + } return pca diff --git a/wqflask/wqflask/templates/correlation_matrix.html b/wqflask/wqflask/templates/correlation_matrix.html index 3da6981c..e90accf2 100644 --- a/wqflask/wqflask/templates/correlation_matrix.html +++ b/wqflask/wqflask/templates/correlation_matrix.html @@ -71,6 +71,12 @@ <button class="btn btn-default" id="export">Download <span class="glyphicon glyphicon-download"></span></button> </form> <br> + +<div style="margin:20x;"> + {% include 'pca_scree_plot.html' %} + +</div> + {% if pca_works == "True" %} <h2>PCA Traits</h2> <div style="margin-bottom: 20px; overflow:hidden; width: 450px;"> diff --git a/wqflask/wqflask/templates/pca_scree_plot.html b/wqflask/wqflask/templates/pca_scree_plot.html index 41036333..11bfebff 100644 --- a/wqflask/wqflask/templates/pca_scree_plot.html +++ b/wqflask/wqflask/templates/pca_scree_plot.html @@ -9,25 +9,25 @@ <body> <div> - pca scree plot + <div id="scree_plot" style="width:700px;height:600px;"></div> </div> </body> <script type="text/javascript" src="{{ url_for('js', filename='plotly/plotly.min.js') }}"></script> <script type="text/javascript"> -js_data = { { js_data | safe } } - +js_data = {{ js_data | safe }} let { x_coord, y_coord } = js_data["scree_data"] + const layout = { title: { - text: "<b>Scree Plot</b>", + text: "<b>Pca Scree Plot</b>", font: { "size": 24, "family": "Arial", - "color": "#FF0000" + "color": "#000000" } }, @@ -77,8 +77,8 @@ let custom_configs = (filename, download_format, modebar = true) => { displayModeBar: modebar, scrollZoom: false, toImageButtonOptions: { - download_format, filename, + format:download_format, height: 600, width: 700, scale: 1 @@ -87,7 +87,7 @@ let custom_configs = (filename, download_format, modebar = true) => { } -Plotly.newPlot(document.getElementById(), data, layout, +Plotly.newPlot(document.getElementById("scree_plot"), data, layout, custom_configs(file_name = "scree_plot", download_format = "svg")); </script> diff --git a/wqflask/wqflask/templates/show_trait_calculate_correlations.html b/wqflask/wqflask/templates/show_trait_calculate_correlations.html index 16a819fa..2f98f14e 100644 --- a/wqflask/wqflask/templates/show_trait_calculate_correlations.html +++ b/wqflask/wqflask/templates/show_trait_calculate_correlations.html @@ -119,9 +119,6 @@ <div class="col-xs-3 controls"> <input type="button" class="btn corr_compute submit_special btn-success" data-url="/corr_compute" title="Compute Correlation" value="Compute"> </div> - <div class="col-xs-3 controls"> - <input type="button" class="btn test_corr_compute submit_special btn-success" data-url="/test_corr_compute" title="Compute Correlation" value="Test Compute"> - </div> </div> </div> </div> |