@jbrowse/plugin-wiggle 1.6.5 → 1.6.6

package/dist/plugin-wiggle.esm.js

@@ -1,7 +1,7 @@
 import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
 import TrackType from '@jbrowse/core/pluggableElementTypes/TrackType';
 import Plugin from '@jbrowse/core/Plugin';
-import { ConfigurationSchema, readConfObject, ConfigurationReference, getConf } from '@jbrowse/core/configuration';
+import { ConfigurationSchema, readConfObject, getConf, ConfigurationReference } from '@jbrowse/core/configuration';
 import { createBaseTrackConfig, createBaseTrackModel } from '@jbrowse/core/pluggableElementTypes/models';
 import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType';
 import FeatureRendererType from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType';
@@ -9,13 +9,13 @@ import { renderToAbstractCanvas } from '@jbrowse/core/util/offscreenCanvasUtils'
 import { observer } from 'mobx-react';
 import React, { useRef, useState, useMemo, lazy } from 'react';
 import { PrerenderedCanvas } from '@jbrowse/core/ui';
-import { featureSpanPx, getSession, isSelectionContainer, isAbortException, getContainingView, renameRegionsIfNeeded, updateStatus } from '@jbrowse/core/util';
+import { featureSpanPx, getContainingView, measureText, getContainingTrack, getSession, isSelectionContainer, isAbortException, renameRegionsIfNeeded, updateStatus } from '@jbrowse/core/util';
 import { scaleLinear, scaleLog, scaleQuantize } from 'd3-scale';
 import { types, getEnv, addDisposer, isAlive } from 'mobx-state-tree';
 import { baseLinearDisplayConfigSchema, BaseLinearDisplayComponent, BaseLinearDisplay } from '@jbrowse/plugin-linear-genome-view';
 import { getRpcSessionId, getFileName } from '@jbrowse/core/util/tracks';
-import { observable, autorun, when } from 'mobx';
-import { Axis, LEFT, RIGHT, axisPropsFromTickScale } from 'react-d3-axis';
+import { autorun, when } from 'mobx';
+import { Axis, LEFT, RIGHT, axisPropsFromTickScale } from 'react-d3-axis-mod';
 import { Portal, makeStyles, alpha, Dialog as Dialog$1, DialogTitle as DialogTitle$1, IconButton as IconButton$1, DialogContent as DialogContent$1, FormControlLabel, Radio, Typography as Typography$1, DialogActions, Button as Button$1 } from '@material-ui/core';
 import { usePopper } from 'react-popper';
 import Color from 'color';
@@ -1614,6 +1614,11 @@ function WiggleConfigFactory(pluginManager) {
       model: types.enumeration('Autoscale type', ['global', 'local', 'globalsd', 'localsd', 'zscore']),
       description: 'global/local using their min/max values or w/ standard deviations (globalsd/localsd)'
     },
+    minimalTicks: {
+      type: 'boolean',
+      defaultValue: false,
+      description: 'use the minimal amount of ticks'
+    },
     minScore: {
       type: 'number',
       defaultValue: Number.MIN_VALUE,
@@ -1681,7 +1686,7 @@ var useStyles = /*#__PURE__*/makeStyles(function (theme) {
       color: theme.palette.common.white,
       fontFamily: theme.typography.fontFamily,
       padding: '4px 8px',
-      fontSize: theme.typography.pxToRem(10),
+      fontSize: theme.typography.pxToRem(12),
       lineHeight: "".concat(round(14 / 10), "em"),
       maxWidth: 300,
       wordWrap: 'break-word'
@@ -1787,25 +1792,32 @@ var YScaleBar = /*#__PURE__*/observer(function (_ref) {
   var model = _ref.model,
       orientation = _ref.orientation;
   var ticks = model.ticks;
-  return React.createElement(Axis, Object.assign({}, ticks, {
+  return ticks ? React.createElement(Axis, Object.assign({}, ticks, {
+    shadow: 2,
     format: function format(n) {
       return n;
     },
     style: {
       orient: orientation === 'left' ? LEFT : RIGHT
     }
-  }));
+  })) : null;
 });
+
 var LinearWiggleDisplay = /*#__PURE__*/observer(function (props) {
   var model = props.model;
   var stats = model.stats,
       height = model.height,
-      needsScalebar = model.needsScalebar;
+      needsScalebar = model.needsScalebar; // @ts-ignore
+
+  var _getContainingView = getContainingView(model),
+      trackLabels = _getContainingView.trackLabels;
+
+  var left = trackLabels === 'overlapping' ? measureText(getConf(getContainingTrack(model), 'name'), 12.8) + 100 : 50;
   return React.createElement("div", null, React.createElement(BaseLinearDisplayComponent, Object.assign({}, props)), stats && needsScalebar ? React.createElement("svg", {
     style: {
       position: 'absolute',
       top: 0,
-      left: 300,
+      left: left,
       pointerEvents: 'none',
       height: height,
       width: 50
@@ -1826,15 +1838,6 @@ var YSCALEBAR_LABEL_OFFSET = 5; // using a map because it preserves order
 
 var rendererTypes = /*#__PURE__*/new Map([['xyplot', 'XYPlotRenderer'], ['density', 'DensityRenderer'], ['line', 'LinePlotRenderer']]);
 
-function logb(x, y) {
-  return Math.log(y) / Math.log(x);
-}
-
-function round$1(v) {
-  var b = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : 1.5;
-  return (v >= 0 ? 1 : -1) * Math.pow(b, 1 + Math.floor(logb(b, Math.abs(v))));
-}
-
 var stateModelFactory = function stateModelFactory(pluginManager, configSchema) {
   return types.compose('LinearWiggleDisplay', BaseLinearDisplay, types.model({
     type: types.literal('LinearWiggleDisplay'),
@@ -1858,17 +1861,25 @@ var stateModelFactory = function stateModelFactory(pluginManager, configSchema)
     return {
       statsReady: false,
       message: undefined,
-      stats: observable({
+      stats: {
         scoreMin: 0,
         scoreMax: 50
-      }),
+      },
       statsFetchInProgress: undefined
     };
   }).actions(function (self) {
     return {
-      updateStats: function updateStats(stats) {
-        self.stats.scoreMin = stats.scoreMin;
-        self.stats.scoreMax = stats.scoreMax;
+      updateStats: function updateStats(_ref) {
+        var scoreMin = _ref.scoreMin,
+            scoreMax = _ref.scoreMax;
+
+        if (self.stats.scoreMin !== scoreMin || self.stats.scoreMax !== scoreMax) {
+          self.stats = {
+            scoreMin: scoreMin,
+            scoreMax: scoreMax
+          };
+        }
+
         self.statsReady = true;
       },
       setColor: function setColor(color) {
@@ -2013,25 +2024,16 @@ var stateModelFactory = function stateModelFactory(pluginManager, configSchema)
             scaleType = self.scaleType,
             minScore = self.minScore,
             maxScore = self.maxScore;
+        var scoreMin = stats.scoreMin,
+            scoreMax = stats.scoreMax;
         var ret = getNiceDomain({
-          domain: [stats.scoreMin, stats.scoreMax],
+          domain: [scoreMin, scoreMax],
           bounds: [minScore, maxScore],
           scaleType: scaleType
-        });
-        var headroom = getConf(self, 'headroom') || 0; // avoid weird scalebar if log value and empty region displayed
+        }); // avoid weird scalebar if log value and empty region displayed
 
         if (scaleType === 'log' && ret[1] === Number.MIN_VALUE) {
           return [0, Number.MIN_VALUE];
-        } // heuristic to just give some extra headroom on bigwig scores if no
-        // maxScore/minScore specified (they have MAX_VALUE/MIN_VALUE if so)
-
-
-        if (maxScore === Number.MAX_VALUE && ret[1] > 1.0) {
-          ret[1] = round$1(ret[1] + headroom);
-        }
-
-        if (minScore === Number.MIN_VALUE && ret[0] < -1.0) {
-          ret[0] = round$1(ret[0] - headroom);
         } // avoid returning a new object if it matches the old value
 
 
@@ -2075,6 +2077,7 @@ var stateModelFactory = function stateModelFactory(pluginManager, configSchema)
         var scaleType = self.scaleType,
             domain = self.domain,
             height = self.height;
+        var minimalTicks = getConf(self, 'minimalTicks');
         var range = [height - YSCALEBAR_LABEL_OFFSET, YSCALEBAR_LABEL_OFFSET];
         var scale = getScale({
           scaleType: scaleType,
@@ -2082,8 +2085,10 @@ var stateModelFactory = function stateModelFactory(pluginManager, configSchema)
           range: range,
           inverted: getConf(self, 'inverted')
         });
-        var ticks = height < 50 ? 2 : 4;
-        return axisPropsFromTickScale(scale, ticks);
+        var ticks = axisPropsFromTickScale(scale, 4);
+        return height < 100 || minimalTicks ? _objectSpread2(_objectSpread2({}, ticks), {}, {
+          values: domain
+        }) : ticks;
       }
 
     };
@@ -2175,10 +2180,10 @@ var stateModelFactory = function stateModelFactory(pluginManager, configSchema)
           })
         }] : []), [{
           label: 'Autoscale type',
-          subMenu: [['local', 'Local']].concat(_toConsumableArray(self.hasGlobalStats ? [['global', 'Global'], ['globalsd', 'Global ± 3σ']] : []), [['localsd', 'Local ± 3σ']]).map(function (_ref) {
-            var _ref2 = _slicedToArray(_ref, 2),
-                val = _ref2[0],
-                label = _ref2[1];
+          subMenu: [['local', 'Local']].concat(_toConsumableArray(self.hasGlobalStats ? [['global', 'Global'], ['globalsd', 'Global ± 3σ']] : []), [['localsd', 'Local ± 3σ']]).map(function (_ref2) {
+            var _ref3 = _slicedToArray(_ref2, 2),
+                val = _ref3[0],
+                label = _ref3[1];
 
             return {
               label: label,
@@ -2492,7 +2497,7 @@ var XYPlotRenderer = /*#__PURE__*/function (_WiggleBaseRenderer) {
           scaleOpts = props.scaleOpts,
           unadjustedHeight = props.height,
           config = props.config,
-          values = props.ticks.values,
+          ticks = props.ticks,
           displayCrossHatches = props.displayCrossHatches;
 
       var _regions = _slicedToArray(regions, 1),
@@ -2536,10 +2541,6 @@ var XYPlotRenderer = /*#__PURE__*/function (_WiggleBaseRenderer) {
           feature: feature
         });
       };
-      ctx.strokeStyle = 'grey';
-      ctx.moveTo(0, toY(0));
-      ctx.lineTo(width, toY(0));
-      ctx.stroke();
       var crossingOrigin = niceMin < pivotValue && niceMax > pivotValue;
 
       var _iterator = _createForOfIteratorHelper(features.values()),
@@ -2614,7 +2615,7 @@ var XYPlotRenderer = /*#__PURE__*/function (_WiggleBaseRenderer) {
       if (displayCrossHatches) {
         ctx.lineWidth = 1;
         ctx.strokeStyle = 'rgba(200,200,200,0.8)';
-        values.forEach(function (tick) {
+        ticks.values.forEach(function (tick) {
           ctx.beginPath();
           ctx.moveTo(0, Math.round(toY(tick)));
           ctx.lineTo(width, Math.round(toY(tick)));
@@ -2838,26 +2839,9 @@ var WiggleGetGlobalStats = /*#__PURE__*/function (_RpcMethodType) {
               case 6:
                 _yield$getAdapter = _context2.sent;
                 dataAdapter = _yield$getAdapter.dataAdapter;
-
-                if (!(dataAdapter instanceof BaseFeatureDataAdapter)) {
-                  _context2.next = 12;
-                  break;
-                }
-
-                if (!dataAdapter.capabilities.includes('hasGlobalStats')) {
-                  _context2.next = 11;
-                  break;
-                }
-
                 return _context2.abrupt("return", dataAdapter.getGlobalStats(deserializedArgs));
 
-              case 11:
-                throw new Error('Data adapter does not support global stats');
-
-              case 12:
-                throw new Error('Data adapter not found');
-
-              case 13:
+              case 9:
               case "end":
                 return _context2.stop();
             }