Merge pull request #199 from lilab-bcb/de-display

de display update
lilab-bcb · Aug 25, 2023 · b55a5cf · b55a5cf
2 parents cde4b1a + 2231f43
commit b55a5cf
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Showing 6 changed files with 689 additions and 642 deletions.
diff --git a/cirrocumulus/job_api.py b/cirrocumulus/job_api.py
@@ -139,9 +139,9 @@ def get_obs(dataset_api, dataset, dataset_info, params):
                 filter_names[i] = "group_" + str(i + 1)
         obs = pd.DataFrame(index=pd.RangeIndex(dataset_info["shape"][0]).astype(str))
         obs_field = "selection"
-        obs[obs_field] = "3"
+        # obs[obs_field] = "3"
         masks, _ = get_mask(dataset_api, dataset, dataset_info, filters)
-        for i in range(len(masks)):
+        for i in range(2):
             obs.loc[masks[i], obs_field] = filter_names[i]
         obs[obs_field] = obs[obs_field].astype("category")
         return obs, obs_field

diff --git a/docs/release_notes.rst b/docs/release_notes.rst
@@ -1,6 +1,9 @@
 Release Notes
 -------------
 
+- 1.1.56 `August 25, 2023`
+    * Updated display for differential expression between two groups
+
 - 1.1.55 `August 16, 2023`
     * Support saving specific fields in `prepare_data` command
 

diff --git a/package.json b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "cirrocumulus",
-  "version": "1.1.55",
+  "version": "1.1.56",
   "private": true,
   "homepage": ".",
   "proxy": "http://127.0.0.1:5000",
@@ -87,7 +87,7 @@
     "jest-puppeteer": "^9.0.0",
     "prettier": "^3.0.0",
     "preval.macro": "^5.0.0",
-    "puppeteer": "^20.9.0"
+    "puppeteer": "^21.1.0"
   },
   "prettier": {
     "bracketSpacing": false,

diff --git a/requirements.txt b/requirements.txt
@@ -1,6 +1,6 @@
 anndata==0.9.2
 CacheControl==0.13.1
-flask==2.3.2
+flask==2.3.3
 flask-compress==1.13
 fsspec==2023.6.0
 gunicorn==21.2.0
@@ -9,7 +9,7 @@ loompy==3.0.7
 numpy==1.25.2
 pandas==2.0.3
 pyarrow==12.0.1
-pymongo==4.4.1
+pymongo==4.5.0
 requests==2.31.0
-scipy==1.11.1
-zarr==2.16.0
+scipy==1.11.2
+zarr==2.16.1
diff --git a/src/DotPlotJobResultsPanel.js b/src/DotPlotJobResultsPanel.js
@@ -55,6 +55,15 @@ export function exportJobResult(jobResult) {
   window.saveAs(blob, jobResult.name + '.tsv');
 }
 
+function getScoreField(fields) {
+  for (let i = 0; i < fields.length; i++) {
+    if (fields[i].toLowerCase().indexOf('score') !== -1) {
+      return fields[i];
+    }
+  }
+  return fields[0]; // default
+}
+
 export function updateJob(jobResult) {
   if (jobResult.type === 'de') {
     if (jobResult.options === undefined) {
@@ -118,19 +127,13 @@ export function updateJob(jobResult) {
       jobResult.byAscending = false;
     }
     if (jobResult.by === undefined) {
-      jobResult.by = jobResult.fields[0];
-      for (let i = 0; i < jobResult.fields.length; i++) {
-        if (jobResult.fields[i].toLowerCase().indexOf('score') !== -1) {
-          jobResult.by = jobResult.fields[i];
-          break;
-        }
-      }
+      jobResult.by = getScoreField(jobResult.fields);
     }
     if (jobResult.sortByGroup === undefined) {
       jobResult.sortByGroup = jobResult.groups[0];
     }
     if (jobResult.color === undefined) {
-      jobResult.color = jobResult.fields[0];
+      jobResult.color = getScoreField(jobResult.fields);
     }
     if (jobResult.size === undefined) {
       jobResult.size = jobResult.fields[0];
@@ -159,7 +162,6 @@ export function updateJob(jobResult) {
       return [min, max];
     }
 
-    // color='logfoldchanges', size='pvals_adj',
     if (jobResult.colorScale === undefined) {
       let domain;
       if (jobResult.interpolator.scale !== INTERPOLATOR_SCALING_NONE) {