Resize plotly (#75)

* Sam/try plots (#71) * Fix batch mode pandas warning. (#70) * refactor to call method on DataFrame, rather than Series. Removes warning. * Fix pandas future warning in CRISPRessoWGS --------- Co-authored-by: Cole Lyman <[email protected]> * Functional * Cole/fix status file name (#69) * Update config file logging messages This removes printing the exception (which is essentially a duplicate), and adds a condition if no config file was provided. Also changes `json` to `config` so that it is more clear. * Fix divide by zero when no amplicons are present in Batch mode * Don't append file_prefix to status file name * Place status files in output directories * Update tests branch for file_prefix addition * Load D3 and plotly figures with pro with multiple amplicons * Update batch * Fix bug in CRISPRessoCompare with pointing to report datas with file_prefix Before this fix, when using a file_prefix the second run that was compared would not be displayed as a data in the first figure of the report. * Import CRISPRessoPro instead of importing the version When installed via conda, the version is not available * Remove `get_amplicon_output` unused function from CRISPRessoCompare Also remove unused argparse import * Implement `get_matching_allele_files` in CRISPRessoCompare and accompanying unit tests * Allow for matching of multiple guides in the same amplicon * Fix pandas FutureWarning * Change test branch back to master --------- Co-authored-by: Sam <[email protected]> * Try catch all futures * Fix test fail plots * Point test to try-plots * Fix d3 not showing and plotly mixing with matplotlib * Use logger for warnings and debug statements * Point tests back at master --------- Co-authored-by: mbowcut2 <[email protected]> Co-authored-by: Cole Lyman <[email protected]> * Sam/fix plots (#72) * Fix batch mode pandas warning. (#70) * refactor to call method on DataFrame, rather than Series. Removes warning. * Fix pandas future warning in CRISPRessoWGS --------- Co-authored-by: Cole Lyman <[email protected]> * Functional * Cole/fix status file name (#69) * Update config file logging messages This removes printing the exception (which is essentially a duplicate), and adds a condition if no config file was provided. Also changes `json` to `config` so that it is more clear. * Fix divide by zero when no amplicons are present in Batch mode * Don't append file_prefix to status file name * Place status files in output directories * Update tests branch for file_prefix addition * Load D3 and plotly figures with pro with multiple amplicons * Update batch * Fix bug in CRISPRessoCompare with pointing to report datas with file_prefix Before this fix, when using a file_prefix the second run that was compared would not be displayed as a data in the first figure of the report. * Import CRISPRessoPro instead of importing the version When installed via conda, the version is not available * Remove `get_amplicon_output` unused function from CRISPRessoCompare Also remove unused argparse import * Implement `get_matching_allele_files` in CRISPRessoCompare and accompanying unit tests * Allow for matching of multiple guides in the same amplicon * Fix pandas FutureWarning * Change test branch back to master --------- Co-authored-by: Sam <[email protected]> * Try catch all futures * Fix test fail plots * Fix d3 not showing and plotly mixing with matplotlib --------- Co-authored-by: mbowcut2 <[email protected]> Co-authored-by: Cole Lyman <[email protected]> * Remove token from integration tests file * Pass div id for plotly * Remove debug --------- Co-authored-by: mbowcut2 <[email protected]> Co-authored-by: Cole Lyman <[email protected]>
edilytics · May 11, 2024 · 17b880a · 17b880a
1 parent 308fd0f
commit 17b880a
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Showing 4 changed files with 33 additions and 8 deletions.
diff --git a/CRISPResso2/CRISPRessoAggregateCORE.py b/CRISPResso2/CRISPRessoAggregateCORE.py
@@ -614,12 +614,14 @@ def main():
                         crispresso2_info['results']['general_plots']['allele_modification_heatmap_plot_titles'] = {}
                         crispresso2_info['results']['general_plots']['allele_modification_heatmap_plot_labels'] = {}
                         crispresso2_info['results']['general_plots']['allele_modification_heatmap_plot_datas'] = {}
+                        crispresso2_info['results']['general_plots']['allele_modification_heatmap_plot_divs'] = {}
 
                         crispresso2_info['results']['general_plots']['allele_modification_line_plot_names'] = []
                         crispresso2_info['results']['general_plots']['allele_modification_line_plot_paths'] = {}
                         crispresso2_info['results']['general_plots']['allele_modification_line_plot_titles'] = {}
                         crispresso2_info['results']['general_plots']['allele_modification_line_plot_labels'] = {}
                         crispresso2_info['results']['general_plots']['allele_modification_line_plot_datas'] = {}
+                        crispresso2_info['results']['general_plots']['allele_modification_line_plot_divs'] = {}
                         if guides_all_same:
                             sgRNA_intervals = [consensus_sgRNA_intervals] * modification_frequency_summary_df.shape[0]
                         else:
@@ -645,11 +647,13 @@ def main():
                             plot_name = 'CRISPRessoAggregate_percentage_of_{0}_across_alleles_{1}_heatmap'.format(modification_type.lower(), amplicon_name)
                             plot_path = '{0}.html'.format(_jp(plot_name))
 
+                            heatmap_div_id = '{0}-allele-modification-heatmap-{1}'.format(amplicon_name.lower(), modification_type.lower())
                             allele_modification_heatmap_input = {
                                 'sample_values': modification_df,
                                 'sample_sgRNA_intervals': sgRNA_intervals,
                                 'plot_path': plot_path,
                                 'title': modification_type,
+                                'div_id': heatmap_div_id,
                             }
                             plot(
                                 CRISPRessoPlot.plot_allele_modification_heatmap,
@@ -671,15 +675,18 @@ def main():
                                     ),
                                 ),
                             ]
+                            crispresso2_info['results']['general_plots']['allele_modification_heatmap_plot_divs'][plot_name] = heatmap_div_id
 
                             plot_name = 'CRISPRessoAggregate_percentage_of_{0}_across_alleles_{1}_line'.format(modification_type.lower(), amplicon_name)
                             plot_path = '{0}.html'.format(_jp(plot_name))
 
+                            line_div_id = '{0}-allele-modification-line-{1}'.format(amplicon_name.lower(), modification_type.lower())
                             allele_modification_line_input = {
                                 'sample_values': modification_df,
                                 'sample_sgRNA_intervals': sgRNA_intervals,
                                 'plot_path': plot_path,
                                 'title': modification_type,
+                                'div_id': line_div_id,
                             }
                             plot(
                                 CRISPRessoPlot.plot_allele_modification_line,
@@ -700,6 +707,7 @@ def main():
                                     ),
                                 ),
                             ]
+                            crispresso2_info['results']['general_plots']['allele_modification_line_plot_divs'][plot_name] = line_div_id
 
             crispresso2_info['results']['general_plots']['window_nuc_pct_quilt_plot_names'] = window_nuc_pct_quilt_plot_names
             crispresso2_info['results']['general_plots']['nuc_pct_quilt_plot_names'] = nuc_pct_quilt_plot_names

diff --git a/CRISPResso2/CRISPRessoBatchCORE.py b/CRISPResso2/CRISPRessoBatchCORE.py
@@ -415,12 +415,14 @@ def main():
         crispresso2_info['results']['general_plots']['allele_modification_heatmap_plot_titles'] = {}
         crispresso2_info['results']['general_plots']['allele_modification_heatmap_plot_labels'] = {}
         crispresso2_info['results']['general_plots']['allele_modification_heatmap_plot_datas'] = {}
+        crispresso2_info['results']['general_plots']['allele_modification_heatmap_plot_divs'] = {}
 
         crispresso2_info['results']['general_plots']['allele_modification_line_plot_names'] = []
         crispresso2_info['results']['general_plots']['allele_modification_line_plot_paths'] = {}
         crispresso2_info['results']['general_plots']['allele_modification_line_plot_titles'] = {}
         crispresso2_info['results']['general_plots']['allele_modification_line_plot_labels'] = {}
         crispresso2_info['results']['general_plots']['allele_modification_line_plot_datas'] = {}
+        crispresso2_info['results']['general_plots']['allele_modification_line_plot_divs'] = {}
 
         percent_complete_start, percent_complete_end = 90, 99
         if all_amplicons:
@@ -798,12 +800,13 @@ def main():
                         plot_name = 'CRISPRessoBatch_percentage_of_{0}_across_alleles_{1}_heatmap'.format(modification_type.lower(), amplicon_name)
                         plot_path = '{0}.html'.format(_jp(plot_name))
 
+                        heatmap_div_id = '{0}-allele-modification-heatmap-{1}'.format(amplicon_name.lower(), modification_type.lower())
                         allele_modification_heatmap_input = {
                             'sample_values': modification_df,
                             'sample_sgRNA_intervals': sgRNA_intervals,
                             'plot_path': plot_path,
                             'title': modification_type,
-                            'amplicon_name': amplicon_name,
+                            'div_id': heatmap_div_id,
                         }
                         debug('Plotting allele modification heatmap for {0}'.format(amplicon_name))
                         plot(
@@ -826,16 +829,18 @@ def main():
                                 ),
                             ),
                         ]
+                        crispresso2_info['results']['general_plots']['allele_modification_heatmap_plot_divs'][plot_name] = heatmap_div_id
 
                         plot_name = 'CRISPRessoBatch_percentage_of_{0}_across_alleles_{1}_line'.format(modification_type.lower(), amplicon_name)
                         plot_path = '{0}.html'.format(_jp(plot_name))
 
+                        line_div_id = '{0}-allele-modification-line-{1}'.format(amplicon_name.lower(), modification_type.lower())
                         allele_modification_line_input = {
                             'sample_values': modification_df,
                             'sample_sgRNA_intervals': sgRNA_intervals,
                             'plot_path': plot_path,
                             'title': modification_type,
-                            'amplicon_name': amplicon_name,
+                            'div_id': line_div_id,
                         }
                         debug('Plotting allele modification line plot for {0}'.format(amplicon_name))
                         plot(
@@ -858,6 +863,7 @@ def main():
                                 ),
                             ),
                         ]
+                        crispresso2_info['results']['general_plots']['allele_modification_line_plot_divs'][plot_name] = line_div_id
             #end if amp_found_count > 0 (how many folders had information for this amplicon)
         #end per-amplicon analysis
 

diff --git a/CRISPResso2/CRISPRessoReports/CRISPRessoReport.py b/CRISPResso2/CRISPRessoReports/CRISPRessoReport.py
@@ -261,6 +261,10 @@ def make_batch_report_from_folder(crispressoBatch_report_file, crispresso2_info,
         allele_modification_heatmap_plot['datas'] = crispresso2_info['results']['general_plots']['allele_modification_heatmap_plot_datas']
     else:
         allele_modification_heatmap_plot['datas'] = {}
+    if 'allele_modification_heatmap_plot_divs' in crispresso2_info['results']['general_plots']:
+        allele_modification_heatmap_plot['divs'] = crispresso2_info['results']['general_plots']['allele_modification_heatmap_plot_divs']
+    else:
+        allele_modification_heatmap_plot['divs'] = {}
 
     allele_modification_line_plot = {}
     if 'allele_modification_line_plot_names' in crispresso2_info['results']['general_plots']:
@@ -283,6 +287,10 @@ def make_batch_report_from_folder(crispressoBatch_report_file, crispresso2_info,
         allele_modification_line_plot['datas'] = crispresso2_info['results']['general_plots']['allele_modification_line_plot_datas']
     else:
         allele_modification_line_plot['datas'] = {}
+    if 'allele_modification_line_plot_divs' in crispresso2_info['results']['general_plots']:
+        allele_modification_line_plot['divs'] = crispresso2_info['results']['general_plots']['allele_modification_line_plot_divs']
+    else:
+        allele_modification_line_plot['divs'] = {}
 
     allele_modification_heatmap_plot['htmls'] = {}
     for heatmap_plot_name, heatmap_plot_path in allele_modification_heatmap_plot['paths'].items():
@@ -572,6 +580,7 @@ def fill_default(dictionary, key, default_type=list):
         ('titles', list),
         ('labels', dict),
         ('datas', dict),
+        ('divs', dict)
     ]
     for dictionary in dictionaries:
         for key, default_type in keys_and_default_types:
@@ -618,11 +627,13 @@ def fill_default(dictionary, key, default_type=list):
             allele_modification_heatmap_plot_titles=allele_modification_heatmap_plot['titles'],
             allele_modification_heatmap_plot_labels=allele_modification_heatmap_plot['labels'],
             allele_modification_heatmap_plot_datas=allele_modification_heatmap_plot['datas'],
+            allele_modification_heatmap_plot_divs=allele_modification_heatmap_plot['divs'],
             allele_modification_line_plot_names=allele_modification_line_plot['names'],
             allele_modification_line_plot_htmls=allele_modification_line_plot['htmls'],
             allele_modification_line_plot_titles=allele_modification_line_plot['titles'],
             allele_modification_line_plot_labels=allele_modification_line_plot['labels'],
             allele_modification_line_plot_datas=allele_modification_line_plot['datas'],
+            allele_modification_line_plot_divs=allele_modification_line_plot['divs'],
             C2PRO_INSTALLED=C2PRO_INSTALLED,
         ))
 

diff --git a/CRISPResso2/CRISPRessoReports/templates/batchReport.html b/CRISPResso2/CRISPRessoReports/templates/batchReport.html
@@ -147,10 +147,10 @@ <h5>{{report_data['titles'][plot_name]}}</h5>
                     <h5>{{allele_modification_heatmap_plot_titles[heatmap_plot_name]}}</h5>
                     <ul class="nav nav-tabs justify-content-center card-header-tabs" id="aln-tab" role="tablist">
                         <li class="nav-item" role="presentation">
-                            <a class="nav-link active" data-bs-toggle="tab" id="{{modification_type}}-heatmap-tab" data-bs-target="#{{heatmap_plot_name}}" role="tab" aria-controls="{{heatmap_plot_name}}" aria-selected="true">Heatmap</a>
+                            <a class="nav-link active" data-bs-toggle="tab" id="{{heatmap_plot_name}}-heatmap-tab" data-bs-target="#{{heatmap_plot_name}}" role="tab" aria-controls="{{heatmap_plot_name}}" aria-selected="true">Heatmap</a>
                         </li>
                         <li class="nav-item" role="presentation">
-                            <a class="nav-link" data-bs-toggle="tab" id="{{modification_type}}-line-tab" data-bs-target="#{{line_plot_name}}" role="tab" aria-controls="{{line_plot_name}}" aria-selected="false">Line</a>
+                            <a class="nav-link" data-bs-toggle="tab" id="{{line_plot_name}}-line-tab" data-bs-target="#{{line_plot_name}}" role="tab" aria-controls="{{line_plot_name}}" aria-selected="false">Line</a>
                         </li>
                     </ul>
                 </div>
@@ -175,13 +175,13 @@ <h5>{{allele_modification_heatmap_plot_titles[heatmap_plot_name]}}</h5>
               </div>
               <script type="application/javascript">
                document.addEventListener("DOMContentLoaded", () => {
-                   $("#{{modification_type}}-heatmap-tab").on("shown.bs.tab", (e) => {
-                       let plot = document.getElementById("allele-modification-heatmap-{{modification_type}}");
+                   $("#{{heatmap_plot_name}}-heatmap-tab").on("shown.bs.tab", (e) => {
+                       let plot = document.getElementById("{{ allele_modification_heatmap_plot_divs[heatmap_plot_name] }}" );
                        Plotly.Plots.resize(plot);
                        window.dispatchEvent(new Event("resize"));
                    });
-                   $("#{{modification_type}}-line-tab").on("shown.bs.tab", (e) => {
-                       let plot = document.getElementById("allele-modification-line-{{modification_type}}");
+                   $("#{{line_plot_name}}-line-tab").on("shown.bs.tab", (e) => {
+                       let plot = document.getElementById("{{ allele_modification_line_plot_divs[line_plot_name] }}");
                        Plotly.Plots.resize(plot);
                        window.dispatchEvent(new Event("resize"));
                    });