Bar graphs: add sort_samples: false config option, also do not sort OrderedDict data

CHANGELOG.md

@@ -14,8 +14,9 @@
 - When trying indexing lists/dicts while accessing config parameters, catch TypeError as well ([#2211](https://github.com/ewels/MultiQC/pull/2211))
 - Fix running `--no-report` ([#2212](https://github.com/ewels/MultiQC/pull/2212))
 - Add `.cram` to sample name cleaning defaults ([#2209](https://github.com/ewels/MultiQC/pull/2209))
-- Fastp: search pattern: look at content instead of file name ([#2213](https://github.com/ewels/MultiQC/pull/2213))
 - Custom content plot: do not assume first row are samples ([#2208](https://github.com/ewels/MultiQC/pull/2208))
+- Fastp: search pattern: look at content instead of file name ([#2213](https://github.com/ewels/MultiQC/pull/2213))
+- Bar graphs: add `sort_samples: false` config option, also do not sort `OrderedDict` data ([#2210](https://github.com/ewels/MultiQC/pull/2210))
 
 ### New Modules
 

docs/core/development/plots.md

@@ -857,7 +857,7 @@ Data and configuration must be added to the document level
 `mqc_plots` variable on page load, using the target as the key.
 The variables used are as follows:
 
-```javascript
+```js
 mqc_plots[target]["plot_type"] = "bar_graph";
 mqc_plots[target]["config"];
 mqc_plots[target]["datasets"];
@@ -866,7 +866,7 @@ mqc_plots[target]["samples"];
 
 All available config options with default vars:
 
-```javascript
+```js
 config = {
   title: undefined, // Plot title
   xlab: undefined, // X axis label
@@ -882,6 +882,7 @@ config = {
   cursor: undefined, // CSS mouse cursor type. Defaults to pointer when 'click_func' specified
   tt_percentages: true, // Show the percentages of each count in the tooltip
   reversedStacks: false, // Reverse the order of the categories in the stack.
+  sort_samples: true, // Sort samples alphanumerically
 };
 ```
 

multiqc/plots/bargraph.py

@@ -7,6 +7,8 @@
 import inspect
 import io
 import logging
+from collections import OrderedDict
+
 import math
 import os
 import random
@@ -135,7 +137,13 @@ def plot(data, cats=None, pconfig=None):
     plotsamples = list()
     plotdata = list()
     for idx, d in enumerate(data):
-        hc_samples = sorted(list(d.keys()))
+        hc_samples = list(d.keys())
+        if isinstance(d, OrderedDict):
+            # Legacy: users assumed that passing an OrderedDict indicates that we
+            # want to keep the sample order https://github.com/ewels/MultiQC/issues/2204
+            pass
+        elif pconfig.get("sort_samples", True):
+            hc_samples = sorted(list(d.keys()))
         hc_data = list()
         sample_dcount = dict()
         for c in cats[idx].keys():