Beeswarm plot: Save data to multiqc_data

Fixes #1861

CHANGELOG.md

@@ -5,6 +5,7 @@
 ### MultiQC updates
 
 - Table code now tolerates lambda function calls with bad data ([#1739](https://github.com/ewels/MultiQC/issues/1739))
+- Beeswarm plot now saves data to `multiqc_data`, same as tables ([#1861](https://github.com/ewels/MultiQC/issues/1861))
 
 ### New Modules
 

multiqc/plots/beeswarm.py

@@ -4,9 +4,10 @@
 
 import logging
 import random
+from collections import defaultdict
 
 from multiqc.plots import table_object
-from multiqc.utils import config, report
+from multiqc.utils import config, report, util_functions
 
 logger = logging.getLogger(__name__)
 
@@ -46,6 +47,7 @@ def make_plot(dt):
     categories = []
     s_names = []
     data = []
+    dt.raw_vals = defaultdict(lambda: dict())
     for idx, hs in enumerate(dt.headers):
         for k, header in hs.items():
             bcol = "rgb({})".format(header.get("colour", "204,204,204"))
@@ -69,6 +71,7 @@ def make_plot(dt):
             for s_name, samp in dt.data[idx].items():
                 if k in samp:
                     val = samp[k]
+                    dt.raw_vals[s_name][k] = val
 
                     if "modify" in header and callable(header["modify"]):
                         val = header["modify"](val)
@@ -95,4 +98,10 @@ def make_plot(dt):
 
     report.plot_data[bs_id] = {"plot_type": "beeswarm", "samples": s_names, "datasets": data, "categories": categories}
 
+    # Save the raw values to a file if requested
+    if dt.pconfig.get("save_file") is True:
+        fn = dt.pconfig.get("raw_data_fn", "multiqc_{}".format(bs_id))
+        util_functions.write_data_file(dt.raw_vals, fn)
+        report.saved_raw_data[fn] = dt.raw_vals
+
     return html