@jbrowse/plugin-wiggle 2.13.0 → 2.14.0

package/esm/util.js

@@ -1,4 +1,4 @@
-import { scaleLinear, scaleLog, scaleQuantize } from 'd3-scale';
+import { scaleLinear, scaleLog, scaleQuantize, } from '@mui/x-charts-vendor/d3-scale';
 import { autorun } from 'mobx';
 import { isAbortException, getSession, getContainingView, } from '@jbrowse/core/util';
 import { getRpcSessionId } from '@jbrowse/core/util/tracks';
@@ -26,8 +26,7 @@ export function getScale({ domain = [], range = [], scaleType, pivotValue, inver
         scale = scaleLinear();
     }
     else if (scaleType === 'log') {
-        scale = scaleLog();
-        scale.base(2);
+        scale = scaleLog().base(2);
     }
     else if (scaleType === 'quantize') {
         scale = scaleQuantize();
@@ -90,17 +89,13 @@ export function getNiceDomain({ scaleType, domain, bounds, }) {
         }
     }
     if (scaleType === 'log') {
-        // if the min is 0, assume that it's just something
-        // with no read coverage and that we should ignore it in calculations
-        // if it's greater than 1 pin to 1 for the full range also
-        // otherwise, we may see bigwigs with fractional values
-        if (min === 0 || min > 1) {
+        // for min>0 and max>1, set log min to 1, which works for most coverage
+        // types tracks. if max is not >1, might be like raw p-values so then it'll
+        // display negative values
+        if (min >= 0 && max > 1) {
             min = 1;
         }
     }
-    if (min === undefined || max === undefined) {
-        throw new Error('invalid domain supplied to stats function');
-    }
     if (minScore !== undefined && minScore !== Number.MIN_VALUE) {
         min = minScore;
     }
@@ -128,7 +123,7 @@ export function getNiceDomain({ scaleType, domain, bounds, }) {
 }
 export async function getQuantitativeStats(self, opts) {
     const { rpcManager } = getSession(self);
-    const nd = getConf(self, 'numStdDev') || 3;
+    const numStdDev = getConf(self, 'numStdDev') || 3;
     const { adapterConfig, autoscaleType } = self;
     const sessionId = getRpcSessionId(self);
     const params = {
@@ -150,8 +145,8 @@ export async function getQuantitativeStats(self, opts) {
         return autoscaleType === 'globalsd'
             ? {
                 ...results,
-                scoreMin: scoreMin >= 0 ? 0 : scoreMean - nd * scoreStdDev,
-                scoreMax: scoreMean + nd * scoreStdDev,
+                scoreMin: scoreMin >= 0 ? 0 : scoreMean - numStdDev * scoreStdDev,
+                scoreMax: scoreMean + numStdDev * scoreStdDev,
             }
             : results;
     }
@@ -176,8 +171,8 @@ export async function getQuantitativeStats(self, opts) {
         return autoscaleType === 'localsd'
             ? {
                 ...results,
-                scoreMin: scoreMin >= 0 ? 0 : scoreMean - nd * scoreStdDev,
-                scoreMax: scoreMean + nd * scoreStdDev,
+                scoreMin: scoreMin >= 0 ? 0 : scoreMean - numStdDev * scoreStdDev,
+                scoreMax: scoreMean + numStdDev * scoreStdDev,
             }
             : results;
     }
@@ -201,6 +196,7 @@ export function quantitativeStatsAutorun(self) {
             const statsRegion = JSON.stringify(view.dynamicBlocks);
             const wiggleStats = await getQuantitativeStats(self, {
                 signal: aborter.signal,
+                filters: [],
                 ...self.renderProps(),
             });
             if (isAlive(self)) {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-wiggle",
-  "version": "2.13.0",
+  "version": "2.14.0",
   "description": "JBrowse 2 wiggle adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -24,7 +24,7 @@
   ],
   "scripts": {
     "build": "npm-run-all build:*",
-    "test": "cd ../..; jest plugins/wiggle",
+    "test": "cd ../..; jest --passWithNoTests plugins/wiggle",
     "prepublishOnly": "yarn test",
     "prepack": "yarn build && yarn useDist",
     "postpack": "yarn useSrc",
@@ -37,12 +37,11 @@
   },
   "dependencies": {
     "@floating-ui/react": "^0.26.3",
-    "@gmod/bbi": "^4.0.0",
+    "@gmod/bbi": "^5.0.0",
     "@mui/icons-material": "^5.0.2",
+    "@mui/x-charts-vendor": "^7.12.0",
     "@mui/x-data-grid": "^7.0.0",
     "clone": "^2.1.2",
-    "d3-color": "^3.0.2",
-    "d3-scale": "^3.0.2",
     "fast-deep-equal": "^3.1.3",
     "is-object": "^1.0.1",
     "react-d3-axis-mod": "^0.1.9",
@@ -66,5 +65,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "efe02fb9616e20e929cceeed46eb96420c1b6923"
+  "gitHead": "9fb8231d932db40adf0a283081765431756c66ff"
 }