Fix "square": True for scatter plot. Make the GATK BaseRecalibrator plot square

CHANGELOG.md

@@ -4,10 +4,14 @@
 
 ### MultiQC updates
 
+- Fix the `"square": True` flag to scatter plot to actually make the plot square ([#2189](https://github.com/ewels/MultiQC/pull/2189))
+
 ### New Modules
 
 ### Module updates
 
+- **GATK**: square the BaseRecalibrator scatter plot ([#2189](https://github.com/ewels/MultiQC/pull/2189))
+
 ## [MultiQC v1.18](https://github.com/ewels/MultiQC/releases/tag/v1.18) - 2023-11-17
 
 ### Highlights

CSP.txt

@@ -2,6 +2,9 @@
 # (Content Security Policy), you will need the following scripts allowlisted:
 
 script-src 'self'
+    # 1.19
+    'sha256-/C57+E7g4T7gJpkhM4cBNKuHqniEVV8thOcQDOUy640=' # multiqc/templates/default/assets/js/multiqc_plotting.js
+
     # 1.18
     'sha256-aY1YMeLr1IxkwxjBe0x60QzbuT4u5Mh/QC6brcAN9Do=' # multiqc/templates/default/assets/js/multiqc_tables.js
 

multiqc/modules/gatk/base_recalibrator.py

@@ -176,6 +176,7 @@ def add_reported_vs_empirical_section(self):
 
             # Build data label configs for this data type
             data_labels.append({"name": "{} Reported vs. Empirical Quality", "ylab": "Empirical quality score"})
+
         plot = scatter.plot(
             sample_data,
             pconfig={
@@ -185,6 +186,9 @@ def add_reported_vs_empirical_section(self):
                 "ylab": "Empirical quality score",
                 "xDecimals": False,
                 "data_labels": data_labels,
+                "xmin": 0,
+                "ymin": 0,
+                "square": True,
             },
         )
 

multiqc/plots/scatter.py

@@ -70,6 +70,18 @@ def plot(data, pconfig=None):
                 d.append(this_series)
         plotdata.append(d)
 
+    if pconfig.get("square"):
+        # Find the max value
+        max_val = 0
+        for d in plotdata:
+            for s in d:
+                max_val = max(max_val, s["x"], s["y"])
+        max_val = 1.02 * max_val  # add 2% padding
+        pconfig["xmax"] = max_val
+        pconfig["ymax"] = max_val
+        # Making sure HighCharts doesn't get creative in adding different paddings
+        pconfig["endOnTick"] = False
+
     # Add on annotation data series
     try:
         if pconfig.get("extra_series"):

multiqc/templates/default/assets/js/multiqc_plotting.js

@@ -981,6 +981,7 @@ function plot_scatter_plot(target, ds) {
         allowDecimals: config["xDecimals"],
         plotBands: config["xPlotBands"],
         plotLines: config["xPlotLines"],
+        endOnTick: config["endOnTick"],
       },
       yAxis: {
         title: {
@@ -995,6 +996,7 @@ function plot_scatter_plot(target, ds) {
         allowDecimals: config["yDecimals"],
         plotBands: config["yPlotBands"],
         plotLines: config["yPlotLines"],
+        endOnTick: config["endOnTick"],
       },
       plotOptions: {
         series: {