Fix no_violin/no_beeswarm flag to table (#2376)

* Fix `no_violin`/`no_beeswarm` flag to table * [automated] Update CHANGELOG.md * Fix docs * Comment and reoder logic --------- Co-authored-by: MultiQC Bot <multiqc-bot@seqera.io>
MultiQC · Feb 25, 2024 · 981715c · 981715c
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commit 981715c
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Showing 9 changed files with 35 additions and 21 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -19,6 +19,7 @@
 - Fix: wrap `full_figure_for_development` in try to handle Kaleido error ([#2359](https://github.com/MultiQC/MultiQC/pull/2359))
 - Generic font family for Plotly ([#2368](https://github.com/MultiQC/MultiQC/pull/2368))
 - Violin plot: filter Inf values ([#2380](https://github.com/MultiQC/MultiQC/pull/2380))
+- Fix use of the `no_violin`/`no_beeswarm` table config flag ([#2376](https://github.com/MultiQC/MultiQC/pull/2376))
 
 ### New modules
 

diff --git a/docs/core/development/plots.md b/docs/core/development/plots.md
@@ -465,7 +465,7 @@ single_header = {
     "cond_formatting_colours": None, # Styles for conditional formatting of table cell values
     "shared_key": None,              # See below for description
     "modify": None,                  # Lambda function to modify values
-    "hidden": False                  # Set to True to hide the column on page load
+    "hidden": False,                 # Set to True to hide the column on page load
 }
 ```
 
@@ -481,7 +481,7 @@ table_config = {
     "sortRows": True,                          # Whether to sort rows alphabetically
     "only_defined_headers": True,              # Only show columns that are defined in the headers config
     "col1_header": "Sample Name",              # The header used for the first column
-    "no_beeswarm": False,                      # Force a table to always be plotted (beeswarm by default if many rows)
+    "no_violin": False,                        # Force a table to always be plotted (beeswarm by default if many rows)
 }
 ```
 

diff --git a/multiqc/modules/bcl2fastq/bcl2fastq.py b/multiqc/modules/bcl2fastq/bcl2fastq.py
@@ -474,7 +474,7 @@ def lane_stats_table(self):
             "id": "bcl2fastq-lane-stats-table",
             "table_title": "bcl2fastq Lane Statistics",
             "col1_header": "Run ID - Lane",
-            "no_beeswarm": True,
+            "no_violin": True,
         }
         return table.plot(self.bcl2fastq_bylane, headers, table_config)
 

diff --git a/multiqc/modules/bclconvert/bclconvert.py b/multiqc/modules/bclconvert/bclconvert.py
@@ -716,7 +716,7 @@ def sample_stats_table(self, bclconvert_data, bclconvert_by_sample):
             "namespace": "bclconvert",
             "id": "bclconvert-sample-stats-table",
             "table_title": "bclconvert Sample Statistics",
-            "no_beeswarm": True,
+            "no_violin": True,
         }
 
         return table.plot(sample_stats_data, headers, table_config)
@@ -822,7 +822,7 @@ def lane_stats_table(self, bclconvert_by_lane):
             "id": "bclconvert-lane-stats-table",
             "table_title": "bclconvert Lane Statistics",
             "col1_header": "Run ID - Lane",
-            "no_beeswarm": True,
+            "no_violin": True,
         }
 
         # new dict with matching keys for plotting (this avoids duplicate html id linting errors)

diff --git a/multiqc/modules/clusterflow/clusterflow.py b/multiqc/modules/clusterflow/clusterflow.py
@@ -152,7 +152,7 @@ def clusterflow_commands_table(self):
             "table_title": "Cluster Flow Commands",
             "col1_header": "Tool",
             "sortRows": False,
-            "no_beeswarm": True,
+            "no_violin": True,
         }
         self.add_section(
             name="Commands",
@@ -336,7 +336,7 @@ def clusterflow_pipelines_section(self):
             "id": "clusterflow-pipelines-table",
             "table_title": "Cluster Flow Pipelines",
             "col1_header": "Pipeline ID",
-            "no_beeswarm": True,
+            "no_violin": True,
             "save_file": True,
         }
         self.add_section(

diff --git a/multiqc/modules/dragen/coverage_metrics.py b/multiqc/modules/dragen/coverage_metrics.py
@@ -470,13 +470,13 @@
     "sortRows": True,  # Whether to sort rows alphabetically
     "only_defined_headers": True,  # Only show columns that are defined in the headers config
     "col1_header": None,  # The header used for the first column with sample names.
-    "no_beeswarm": False,  # Force a table to always be plotted (beeswarm by default if many rows)
+    "no_violin": False,  # Force a table to always be plotted (beeswarm by default if many rows)
 }
 # Below are region-specific configs with higher priority.
 REGION_TABLE_CONFIG = {
     WGS: {
         "table_title": "WGS",
-        # "no_beeswarm": True,
+        # "no_violin": True,
         # "save_file": True,
         # "raw_data_fn": "Genome_raw_file",
     },

diff --git a/multiqc/modules/picard/CrosscheckFingerprints.py b/multiqc/modules/picard/CrosscheckFingerprints.py
@@ -107,7 +107,7 @@ def parse_reports(module):
                 "table_title": f"{module.name}: Crosscheck Fingerprints",
                 "save_file": True,
                 "col1_header": "ID",
-                "no_beeswarm": True,
+                "no_violin": True,
             },
         ),
     )

diff --git a/multiqc/modules/somalier/somalier.py b/multiqc/modules/somalier/somalier.py
@@ -391,7 +391,7 @@ def somalier_stats_table(self):
             "id": "somalier_stats",
             "namespace": "Somalier",
             "title": "Somalier: Statistics",
-            "no_beeswarm": True,
+            "no_violin": True,
             "raw_data_fn": "multiqc_somalier_stats",
         }
 

diff --git a/multiqc/plots/plotly/violin.py b/multiqc/plots/plotly/violin.py
@@ -328,8 +328,9 @@ def __init__(
         assert len(list_of_values_by_sample_by_metric) > 0
 
         self.dt = dt
-        self.show_table_by_default = dt is not None and show_table_by_default
+        self.no_violin = pconfig.get("no_violin", pconfig.get("no_beeswarm", False))
         self.show_table = dt is not None
+        self.show_table_by_default = show_table_by_default or self.no_violin
 
         super().__init__(
             PlotType.VIOLIN,
@@ -381,7 +382,7 @@ def __init__(
         # - plot a Violin in Python, and serialise the figure instead of the datasets
         self.n_samples = max(len(ds.all_samples) for ds in self.datasets)
         self.serialize_figure = False
-        if self.n_samples > config.max_table_rows:
+        if self.n_samples > config.max_table_rows and not self.no_violin:
             self.show_table = False
             if self.show_table_by_default:
                 logger.debug(
@@ -431,7 +432,10 @@ def tt_label() -> str:
         return ": %{x}"
 
     def add_to_report(self, report) -> str:
-        violin_html = super().add_to_report(report)
+        if not self.no_violin:
+            violin_html = super().add_to_report(report)
+        else:
+            violin_html = ""
 
         warning = ""
         if self.show_table_by_default and not self.show_table:
@@ -456,17 +460,26 @@ def add_to_report(self, report) -> str:
             )
 
         if not self.show_table:
-            # Show violin alone
+            # Show violin alone.
+            # Note that "no_violin" will be ignored here as we need to render _something_. The only case it can
+            # happen if violin.plot() is called directly, and "no_violin" is passed, which doesn't make sense.
             html = warning + violin_html
+        elif self.no_violin:
+            # Show table alone
+            table_html, configuration_modal = make_table(self.dt)
+            html = warning + table_html + configuration_modal
         else:
-            # Switch between table and violin
+            # Render both, add a switch between table and violin
             table_html, configuration_modal = make_table(self.dt, violin_id=self.id)
-            visibility = "style='display: none;'" if self.show_table_by_default else ""
-            html = f"<div id='mqc_violintable_wrapper_{self.id}' {visibility}>{warning}{violin_html}</div>"
-            if self.show_table:
-                visibility = "style='display: none;'" if not self.show_table_by_default else ""
-                html += f"<div id='mqc_violintable_wrapper_{self.dt.id}' {visibility}>{table_html}</div>"
+
+            violin_visibility = "style='display: none;'" if self.show_table_by_default else ""
+            html = f"<div id='mqc_violintable_wrapper_{self.id}' {violin_visibility}>{warning}{violin_html}</div>"
+
+            table_visibility = "style='display: none;'" if not self.show_table_by_default else ""
+            html += f"<div id='mqc_violintable_wrapper_{self.dt.id}' {table_visibility}>{table_html}</div>"
+
             html += configuration_modal
+
         return html
 
     def dump_for_javascript(self):