Showing sgRNA sequences on hover in CRISPRessoPro (pinellolab#432)

* Passing sgRNA sequences to regular and Batch D3 plots (#73) * 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 <cole@colelyman.com> * 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 <snic9004@gmail.com> * 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 <55161542+mbowcut2@users.noreply.github.com> Co-authored-by: Cole Lyman <cole@colelyman.com> * 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 <cole@colelyman.com> * 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 <snic9004@gmail.com> * Try catch all futures * Fix test fail plots * Fix d3 not showing and plotly mixing with matplotlib --------- Co-authored-by: mbowcut2 <55161542+mbowcut2@users.noreply.github.com> Co-authored-by: Cole Lyman <cole@colelyman.com> * Remove token from integration tests file * Provide sgRNA_sequences to plot_nucleotide_quilt plots * Passing sgRNA_sequences to plot * Refactor check for determining when to use CRISPREssoPro or matplotlib for Batch plots * Add max-height to Batch report samples * Change testing branch * Fix wrong check for large Batch plots * Update integration_tests.yml to point back at master --------- Co-authored-by: Samuel Nichols <Snic9004@gmail.com> Co-authored-by: mbowcut2 <55161542+mbowcut2@users.noreply.github.com> Co-authored-by: Cole Lyman <cole@colelyman.com> * Push new releases to ECR (#74) * Create aws_ecr.yml (#1) * Update aws_ecr.yml * Update aws_ecr.yml * Update aws_ecr.yml * Update aws_ecr.yml * Update aws_ecr.yml * Update aws_ecr.yml * Update aws_ecr.yml * Update aws_ecr.yml * Update aws_ecr.yml * Update aws_ecr.yml * Update aws_ecr.yml * Update aws_ecr.yml * Update aws_ecr.yml * Update aws_ecr.yml * Update aws_ecr.yml * Update aws_ecr.yml * Update aws_ecr.yml * Update aws_ecr.yml * Update aws_ecr.yml * Update aws_ecr.yml * Update aws_ecr.yml * Update aws_ecr.yml * us-east-1 * Update aws_ecr.yml * Update aws_ecr.yml * Update aws_ecr.yml * Update aws_ecr.yml * Update aws_ecr.yml * Fix d3 sgRNA sequences (#76) * Pass correct sgRNA_sequences to d3 plot * Pass correct sgRNA sequence to prime editor plot for d3 * 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 <cole@colelyman.com> * 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 <snic9004@gmail.com> * 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 <55161542+mbowcut2@users.noreply.github.com> Co-authored-by: Cole Lyman <cole@colelyman.com> * 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 <cole@colelyman.com> * 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 <snic9004@gmail.com> * Try catch all futures * Fix test fail plots * Fix d3 not showing and plotly mixing with matplotlib --------- Co-authored-by: mbowcut2 <55161542+mbowcut2@users.noreply.github.com> Co-authored-by: Cole Lyman <cole@colelyman.com> * Remove token from integration tests file * Pass div id for plotly * Remove debug --------- Co-authored-by: mbowcut2 <55161542+mbowcut2@users.noreply.github.com> Co-authored-by: Cole Lyman <cole@colelyman.com> --------- Co-authored-by: Trevor Martin <60452953+trevormartinj7@users.noreply.github.com> Co-authored-by: Samuel Nichols <Snic9004@gmail.com> Co-authored-by: mbowcut2 <55161542+mbowcut2@users.noreply.github.com>
edilytics · Nov 8, 2024 · 3891baf · 3891baf
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Showing 6 changed files with 15 additions and 14 deletions.
diff --git a/.github/workflows/aws_ecr.yml b/.github/workflows/aws_ecr.yml
@@ -38,7 +38,7 @@ jobs:
         AWS_ACCOUNT: ${{ secrets.AWS_ACCOUNT_ID }}
         ECR_REPOSITORY: 'crispresso2'
         AWS_REGION: 'us-east-1'
-        IMAGE_TAG: v${{ steps.get_version.outputs.version }}
+        IMAGE_TAG: ${{ steps.get_version.outputs.version }}
       run: |
         # Build a docker container and push it to ECR 
         docker build -t $AWS_ACCOUNT.dkr.ecr.$AWS_REGION.amazonaws.com/$ECR_REPOSITORY:$IMAGE_TAG .

diff --git a/CRISPResso2/CRISPRessoBatchCORE.py b/CRISPResso2/CRISPRessoBatchCORE.py
@@ -424,8 +424,6 @@ def main():
         crispresso2_info['results']['general_plots']['allele_modification_line_plot_datas'] = {}
         crispresso2_info['results']['general_plots']['allele_modification_line_plot_divs'] = {}
 
-        large_plot_cutoff = 300
-
         percent_complete_start, percent_complete_end = 90, 99
         if all_amplicons:
             percent_complete_step = (percent_complete_end - percent_complete_start) / len(all_amplicons)
@@ -609,7 +607,7 @@ def main():
                         sub_modification_percentage_summary_filename = _jp(amplicon_plot_name + 'Modification_percentage_summary_around_sgRNA_'+sgRNA+'.txt')
                         sub_modification_percentage_summary_df.to_csv(sub_modification_percentage_summary_filename, sep='\t', index=None)
 
-                        if not args.suppress_plots and not args.suppress_batch_summary_plots and (nucleotide_percentage_summary_df.shape[0] / 6) < large_plot_cutoff:
+                        if not args.suppress_plots and not args.suppress_batch_summary_plots and should_plot_large_plots(sub_nucleotide_percentage_summary_df.shape[0], C2PRO_INSTALLED, args.use_matplotlib):
                             # plot for each guide
                             # show all sgRNA's on the plot
                             sub_sgRNA_intervals = []
@@ -658,7 +656,7 @@ def main():
                             crispresso2_info['results']['general_plots']['summary_plot_labels'][plot_name] = 'Composition of each base around the guide ' + sgRNA + ' for the amplicon ' + amplicon_name
                             crispresso2_info['results']['general_plots']['summary_plot_datas'][plot_name] = [('Nucleotide frequencies', os.path.basename(nucleotide_frequency_summary_filename)), ('Modification frequencies', os.path.basename(modification_frequency_summary_filename))]
 
-                            if args.base_editor_output and (sub_nucleotide_percentage_summary_df.shape[0] / 6) < large_plot_cutoff:
+                            if args.base_editor_output and should_plot_large_plots(sub_nucleotide_percentage_summary_df.shape[0], False, args.use_matplotlib):
                                 this_window_nuc_conv_plot_name = _jp(amplicon_plot_name + 'Nucleotide_conversion_map_around_sgRNA_'+sgRNA)
                                 conversion_map_input = {
                                     'nuc_pct_df': sub_nucleotide_percentage_summary_df,
@@ -686,7 +684,7 @@ def main():
                                                                                 ]
                         # done with per-sgRNA plots
 
-                    if not args.suppress_plots and not args.suppress_batch_summary_plots:  # plot the whole region
+                    if not args.suppress_plots and not args.suppress_batch_summary_plots and should_plot_large_plots(nucleotide_percentage_summary_df.shape[0], C2PRO_INSTALLED, args.use_matplotlib):  # plot the whole region
                         this_nuc_pct_quilt_plot_name = _jp(amplicon_plot_name.replace('.', '') + 'Nucleotide_percentage_quilt')
                         nucleotide_quilt_input = {
                             'nuc_pct_df': nucleotide_percentage_summary_df,
@@ -710,7 +708,7 @@ def main():
                             crispresso2_info['results']['general_plots']['summary_plot_titles'][plot_name] = ''
                         crispresso2_info['results']['general_plots']['summary_plot_labels'][plot_name] = 'Composition of each base for the amplicon ' + amplicon_name
                         crispresso2_info['results']['general_plots']['summary_plot_datas'][plot_name] = [('Nucleotide frequencies', os.path.basename(nucleotide_frequency_summary_filename)), ('Modification frequencies', os.path.basename(modification_frequency_summary_filename))]
-                        if args.base_editor_output and (sub_nucleotide_percentage_summary_df.shape[0] / 6) < large_plot_cutoff:
+                        if args.base_editor_output and should_plot_large_plots(nucleotide_percentage_summary_df.shape[0], False, args.use_matplotlib):
                             this_nuc_conv_plot_name = _jp(amplicon_plot_name + 'Nucleotide_conversion_map')
                             conversion_map_input = {
                                 'nuc_pct_df': nucleotide_percentage_summary_df,
@@ -737,7 +735,7 @@ def main():
                             crispresso2_info['results']['general_plots']['summary_plot_datas'][plot_name] = [('Nucleotide frequencies', os.path.basename(nucleotide_frequency_summary_filename)), ('Modification frequencies', os.path.basename(modification_frequency_summary_filename))]
 
                 else:  # guides are not the same
-                    if not args.suppress_plots and not args.suppress_batch_summary_plots:
+                    if not args.suppress_plots and not args.suppress_batch_summary_plots and should_plot_large_plots(nucleotide_percentage_summary_df.shape[0], C2PRO_INSTALLED, args.use_matplotlib):
                         this_nuc_pct_quilt_plot_name = _jp(amplicon_plot_name.replace('.', '') + 'Nucleotide_percentage_quilt')
                         nucleotide_quilt_input = {
                             'nuc_pct_df': nucleotide_percentage_summary_df,
@@ -755,7 +753,7 @@ def main():
                         nuc_pct_quilt_plot_names.append(plot_name)
                         crispresso2_info['results']['general_plots']['summary_plot_labels'][plot_name] = 'Composition of each base for the amplicon ' + amplicon_name
                         crispresso2_info['results']['general_plots']['summary_plot_datas'][plot_name] = [('Nucleotide frequencies', os.path.basename(nucleotide_frequency_summary_filename)), ('Modification frequencies', os.path.basename(modification_frequency_summary_filename))]
-                        if args.base_editor_output and (sub_nucleotide_percentage_summary_df.shape[0] / 6) < large_plot_cutoff:
+                        if args.base_editor_output and should_plot_large_plots(nucleotide_percentage_summary_df.shape[0], False, args.use_matplotlib):
                             this_nuc_conv_plot_name = _jp(amplicon_plot_name + 'Nucleotide_percentage_quilt')
                             conversion_map_input = {
                                 'nuc_pct_df': nucleotide_percentage_summary_df,
@@ -776,7 +774,7 @@ def main():
                             crispresso2_info['results']['general_plots']['summary_plot_datas'][plot_name] = [('Nucleotide frequencies', os.path.basename(nucleotide_frequency_summary_filename)), ('Modification frequencies', os.path.basename(modification_frequency_summary_filename))]
 
                 # allele modification frequency heatmap and line plots
-                if C2PRO_INSTALLED and not args.use_matplotlib and not args.suppress_plots and not args.suppress_batch_summary_plots and (nucleotide_percentage_summary_df.shape[0] / 6) < large_plot_cutoff:
+                if C2PRO_INSTALLED and not args.use_matplotlib and not args.suppress_plots and not args.suppress_batch_summary_plots:
                     if guides_all_same:
                         sgRNA_intervals = [consensus_sgRNA_intervals] * modification_frequency_summary_df.shape[0]
                     else:
@@ -808,7 +806,7 @@ def main():
                             '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(
@@ -842,7 +840,7 @@ def main():
                             '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(

diff --git a/CRISPResso2/CRISPRessoCORE.py b/CRISPResso2/CRISPRessoCORE.py
@@ -4207,6 +4207,7 @@ def count_alternate_alleles(sub_base_vectors, ref_name, ref_sequence, ref_total_
                         'quantification_window_idxs': include_idxs_list,
                         'sgRNA_names': sgRNA_names,
                         'sgRNA_mismatches': sgRNA_mismatches,
+                        'sgRNA_sequences': sgRNA_sequences,
                         'custom_colors': custom_config["colors"],
                     }
                     debug('Plotting HDR nucleotide quilt')
@@ -4792,6 +4793,7 @@ def get_scaffold_len(row, scaffold_start_loc, scaffold_seq):
                 sgRNA_intervals = refs[ref_names[0]]['sgRNA_intervals']
                 sgRNA_names = refs[ref_names[0]]['sgRNA_names']
                 sgRNA_mismatches = refs[ref_names[0]]['sgRNA_mismatches']
+                sgRNA_sequences = refs[ref_names[0]]['sgRNA_sequences']
                 include_idxs_list = refs[ref_names[0]]['include_idxs']
 
                 plot_root = _jp('11a.Prime_editing_nucleotide_percentage_quilt')

diff --git a/CRISPResso2/CRISPRessoReports/CRISPRessoReport.py b/CRISPResso2/CRISPRessoReports/CRISPRessoReport.py
@@ -633,6 +633,7 @@ def fill_default(dictionary, key, default_type=list):
             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
@@ -58,7 +58,7 @@
                 <h5 id="CRISPResso2_Batch_Output">{{report_name}}</h5>
               </div>
               <div class='card-body p-0'>
-                <div class="list-group list-group-flush">
+                <div class="list-group list-group-flush" style="max-height: 25vh; overflow-y: scroll;">
               {% for run_name in run_names %}
 	      <a href="{{sub_html_files[run_name]}}" class="list-group-item list-group-item-action" id="{{run_name}}">{{run_name}}</a>
                 {% endfor %}

diff --git a/CRISPResso2/CRISPRessoReports/templates/shared/partials/failed_runs.html b/CRISPResso2/CRISPRessoReports/templates/shared/partials/failed_runs.html
@@ -9,7 +9,7 @@ <h5 id="failed_runs" class="mb-0 text-white">Failed Runs</h5>
     </div>
 
     <div class='card-body p-0'>
-      <div class="list-group list-group-flush">
+      <div class="list-group list-group-flush" style="max-height: 25vh; overflow-y: scroll;">
         {% for failed_run in failed_runs %}
         {# Toggle the description visibility on click #}
         <a href="javascript:void(0)" class="list-group-item list-group-item-action failed-run-name bg-light text-dark"