@jbrowse/plugin-wiggle 1.7.11 → 2.1.0

package/src/MultiLineRenderer/configSchema.ts

@@ -0,0 +1,24 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration'
+import { types } from 'mobx-state-tree'
+import ConfigSchema from '../configSchema'
+
+const configSchema = ConfigurationSchema(
+  'MultiLineRenderer',
+  {
+    displayCrossHatches: {
+      type: 'boolean',
+      description: 'choose to draw cross hatches (sideways lines)',
+      defaultValue: false,
+    },
+
+    summaryScoreMode: {
+      type: 'stringEnum',
+      model: types.enumeration('Score type', ['max', 'min', 'avg', 'whiskers']),
+      description:
+        'choose whether to use max/min/average or whiskers which combines all three into the same rendering',
+      defaultValue: 'avg',
+    },
+  },
+  { baseConfiguration: ConfigSchema, explicitlyTyped: true },
+)
+export default configSchema

package/src/MultiLineRenderer/index.ts

@@ -0,0 +1,17 @@
+import PluginManager from '@jbrowse/core/PluginManager'
+
+import ReactComponent from '../MultiWiggleRendering'
+import MultiLineRenderer from './MultiLineRenderer'
+import configSchema from './configSchema'
+
+export default (pluginManager: PluginManager) => {
+  pluginManager.addRendererType(
+    () =>
+      new MultiLineRenderer({
+        name: 'MultiLineRenderer',
+        ReactComponent,
+        configSchema,
+        pluginManager,
+      }),
+  )
+}

package/src/MultiLinearWiggleDisplay/components/SetColorDialog.tsx

@@ -0,0 +1,322 @@
+import React, { useState } from 'react'
+import {
+  Button,
+  Dialog,
+  DialogContent,
+  DialogActions,
+  DialogTitle,
+  IconButton,
+  Paper,
+  PaperProps,
+} from '@mui/material'
+import { makeStyles } from 'tss-react/mui'
+import {
+  getStr,
+  isUriLocation,
+  measureGridWidth,
+  useLocalStorage,
+} from '@jbrowse/core/util'
+import { DataGrid, GridCellParams } from '@mui/x-data-grid'
+import Draggable from 'react-draggable'
+import clone from 'clone'
+
+// locals
+import ColorPicker, { ColorPopover } from '@jbrowse/core/ui/ColorPicker'
+import { UriLink } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail'
+import { moveUp, moveDown } from './util'
+import { Source } from '../../util'
+
+// icons
+import CloseIcon from '@mui/icons-material/Close'
+import KeyboardDoubleArrowUpIcon from '@mui/icons-material/KeyboardDoubleArrowUp'
+import KeyboardDoubleArrowDownIcon from '@mui/icons-material/KeyboardDoubleArrowDown'
+import KeyboardArrowDownIcon from '@mui/icons-material/KeyboardArrowDown'
+import KeyboardArrowUpIcon from '@mui/icons-material/KeyboardArrowUp'
+
+const useStyles = makeStyles()(theme => ({
+  closeButton: {
+    position: 'absolute',
+    right: theme.spacing(1),
+    top: theme.spacing(1),
+    color: theme.palette.grey[500],
+  },
+  content: {
+    minWidth: 800,
+  },
+}))
+
+// draggable dialog demo https://mui.com/material-ui/react-dialog/#draggable-dialog
+function PaperComponent(props: PaperProps) {
+  return (
+    <Draggable
+      handle="#draggable-dialog-title"
+      cancel={'[class*="MuiDialogContent-root"]'}
+    >
+      <Paper {...props} />
+    </Draggable>
+  )
+}
+export default function SetColorDialog({
+  model,
+  handleClose,
+}: {
+  model: {
+    sources: Source[]
+    setLayout: (s: Source[]) => void
+    clearLayout: () => void
+  }
+  handleClose: () => void
+}) {
+  const { classes } = useStyles()
+  const { sources } = model
+  const [currLayout, setCurrLayout] = useState(clone(sources || []))
+  const [showTipsTmp, setShowTips] = useLocalStorage(
+    'multiwiggle-showTips',
+    'true',
+  )
+  const showTips = showTipsTmp === 'true'
+  return (
+    <Dialog
+      PaperComponent={PaperComponent}
+      open
+      onClose={handleClose}
+      maxWidth="xl"
+      aria-labelledby="draggable-dialog-title" // this area is important for the draggable functionality
+    >
+      <DialogTitle style={{ cursor: 'move' }} id="draggable-dialog-title">
+        Multi-wiggle color/arrangement editor{' '}
+        <IconButton className={classes.closeButton} onClick={handleClose}>
+          <CloseIcon />
+        </IconButton>
+      </DialogTitle>
+      <DialogContent className={classes.content}>
+        <Button
+          variant="contained"
+          style={{ float: 'right' }}
+          onClick={() => setShowTips(showTips ? 'false' : 'true')}
+        >
+          {showTips ? 'Hide tips' : 'Show tips'}
+        </Button>
+        <br />
+        {showTips ? (
+          <>
+            Helpful tips
+            <ul>
+              <li>You can select rows in the table with the checkboxes</li>
+              <li>
+                Multi-select is enabled with shift-click and control-click
+              </li>
+              <li>
+                The "Move selected items up/down" can re-arrange subtracks
+              </li>
+              <li>
+                Sorting the data grid itself can also re-arrange subtracks
+              </li>
+              <li>Changes are applied when you hit Submit</li>
+              <li>
+                You can click and drag the dialog box to move it on the screen
+              </li>
+              <li>
+                Columns in the table can be hidden using a vertical '...' menu
+                on the right side of each column
+              </li>
+            </ul>
+          </>
+        ) : null}
+        <SourcesGrid
+          rows={currLayout}
+          onChange={setCurrLayout}
+          showTips={showTips}
+        />
+      </DialogContent>
+      <DialogActions>
+        <Button
+          variant="contained"
+          type="submit"
+          color="inherit"
+          onClick={() => {
+            model.clearLayout()
+            setCurrLayout(model.sources)
+          }}
+        >
+          Clear custom settings
+        </Button>
+        <Button
+          variant="contained"
+          color="secondary"
+          onClick={() => {
+            handleClose()
+            setCurrLayout([...model.sources])
+          }}
+        >
+          Cancel
+        </Button>
+        <Button
+          variant="contained"
+          color="primary"
+          type="submit"
+          onClick={() => {
+            model.setLayout(currLayout)
+            handleClose()
+          }}
+        >
+          Submit
+        </Button>
+      </DialogActions>
+    </Dialog>
+  )
+}
+
+function SourcesGrid({
+  rows,
+  onChange,
+  showTips,
+}: {
+  rows: Source[]
+  onChange: (arg: Source[]) => void
+  showTips: boolean
+}) {
+  const [anchorEl, setAnchorEl] = useState<HTMLElement | null>(null)
+  const [selected, setSelected] = useState([] as string[])
+
+  // @ts-ignore
+  const { name: _name, color: _color, baseUri: _baseUri, ...rest } = rows[0]
+
+  // similar to BaseFeatureDetail data-grid for auto-measuring columns
+  const columns = [
+    {
+      field: 'color',
+      headerName: 'Color',
+      renderCell: (params: GridCellParams) => {
+        const { value, id } = params
+        return (
+          <ColorPicker
+            color={value || 'blue'}
+            onChange={c => {
+              const elt = rows.find(f => f.name === id)
+              if (elt) {
+                elt.color = c
+              }
+              onChange([...rows])
+            }}
+          />
+        )
+      },
+    },
+    {
+      field: 'name',
+      sortingOrder: [null],
+      headerName: 'Name',
+      width: measureGridWidth(rows.map(r => r.name)),
+    },
+    ...Object.keys(rest).map(val => ({
+      field: val,
+      sortingOrder: [null],
+      renderCell: (params: GridCellParams) => {
+        const { value } = params
+        return isUriLocation(value) ? <UriLink value={value} /> : getStr(value)
+      },
+      // @ts-ignore
+      width: measureGridWidth(rows.map(r => r[val])),
+    })),
+  ]
+
+  // this helps keep track of the selection, even though it is not used
+  // anywhere except inside the picker
+  const [widgetColor, setWidgetColor] = useState('blue')
+  const [currSort, setCurrSort] = useState<{
+    idx: number
+    field: string | null
+  }>({ idx: 0, field: null })
+
+  return (
+    <div>
+      <Button
+        disabled={!selected.length}
+        onClick={event => setAnchorEl(event.currentTarget)}
+      >
+        Change color of selected items
+      </Button>
+      <Button
+        onClick={() => onChange(moveUp([...rows], selected))}
+        disabled={!selected.length}
+      >
+        <KeyboardArrowUpIcon />
+        {showTips ? 'Move selected items up' : null}
+      </Button>
+      <Button
+        onClick={() => onChange(moveDown([...rows], selected))}
+        disabled={!selected.length}
+      >
+        <KeyboardArrowDownIcon />
+        {showTips ? 'Move selected items down' : null}
+      </Button>
+      <Button
+        onClick={() => onChange(moveUp([...rows], selected, rows.length))}
+        disabled={!selected.length}
+      >
+        <KeyboardDoubleArrowUpIcon />
+        {showTips ? 'Move selected items to top' : null}
+      </Button>
+      <Button
+        onClick={() => onChange(moveDown([...rows], selected, rows.length))}
+        disabled={!selected.length}
+      >
+        <KeyboardDoubleArrowDownIcon />
+        {showTips ? 'Move selected items to bottom' : null}
+      </Button>
+      <ColorPopover
+        anchorEl={anchorEl}
+        color={widgetColor}
+        onChange={c => {
+          setWidgetColor(c)
+          selected.forEach(id => {
+            const elt = rows.find(f => f.name === id)
+            if (elt) {
+              elt.color = c
+            }
+          })
+
+          onChange([...rows])
+        }}
+        onClose={() => setAnchorEl(null)}
+      />
+      <div style={{ height: 400, width: '100%' }}>
+        <DataGrid
+          getRowId={row => row.name}
+          checkboxSelection
+          disableSelectionOnClick
+          onSelectionModelChange={arg => setSelected(arg as string[])}
+          rows={rows}
+          rowHeight={25}
+          headerHeight={33}
+          columns={columns}
+          sortModel={
+            [
+              /* we control the sort as a controlled component using onSortModelChange */
+            ]
+          }
+          onSortModelChange={args => {
+            const sort = args[0]
+            const idx = (currSort.idx + 1) % 2
+            const field = sort?.field || currSort.field
+            setCurrSort({ idx, field })
+            onChange(
+              field
+                ? [...rows].sort((a, b) => {
+                    // @ts-ignore
+                    const aa = getStr(a[field])
+                    // @ts-ignore
+                    const bb = getStr(b[field])
+                    return idx === 1
+                      ? aa.localeCompare(bb)
+                      : bb.localeCompare(aa)
+                  })
+                : rows,
+            )
+          }}
+        />
+      </div>
+    </div>
+  )
+}

package/src/MultiLinearWiggleDisplay/components/SetMinMaxDialog.tsx

@@ -0,0 +1,113 @@
+import React, { useState } from 'react'
+import {
+  Button,
+  Dialog,
+  DialogContent,
+  DialogTitle,
+  IconButton,
+  TextField,
+  Typography,
+} from '@mui/material'
+import { makeStyles } from 'tss-react/mui'
+import CloseIcon from '@mui/icons-material/Close'
+
+const useStyles = makeStyles()(theme => ({
+  root: {},
+  closeButton: {
+    position: 'absolute',
+    right: theme.spacing(1),
+    top: theme.spacing(1),
+    color: theme.palette.grey[500],
+  },
+}))
+
+export default function SetMinMaxDlg(props: {
+  model: {
+    minScore: number
+    maxScore: number
+    scaleType: string
+    setMinScore: Function
+    setMaxScore: Function
+  }
+  handleClose: () => void
+}) {
+  const { classes } = useStyles()
+  const { model, handleClose } = props
+  const { minScore, maxScore, scaleType } = model
+
+  const [min, setMin] = useState(
+    `${minScore !== Number.MIN_VALUE ? minScore : ''}`,
+  )
+  const [max, setMax] = useState(
+    `${maxScore !== Number.MAX_VALUE ? maxScore : ''}`,
+  )
+
+  const ok =
+    min !== '' && max !== '' && !Number.isNaN(+min) && !Number.isNaN(+max)
+      ? +max > +min
+      : true
+
+  const logOk =
+    scaleType === 'log' && min !== '' && !Number.isNaN(+min) ? +min > 0 : true
+
+  return (
+    <Dialog open onClose={handleClose}>
+      <DialogTitle>
+        Set min/max score for track
+        <IconButton className={classes.closeButton} onClick={handleClose}>
+          <CloseIcon />
+        </IconButton>
+      </DialogTitle>
+      <DialogContent style={{ overflowX: 'hidden' }}>
+        <div className={classes.root}>
+          <Typography>Enter min/max score: </Typography>
+          {!ok ? (
+            <Typography color="error">
+              Max is greater than or equal to min
+            </Typography>
+          ) : null}
+
+          {!logOk ? (
+            <Typography color="error">
+              Min score should be greater than 0 for log scale
+            </Typography>
+          ) : null}
+
+          <TextField
+            value={min}
+            onChange={event => {
+              setMin(event.target.value)
+            }}
+            placeholder="Enter min score"
+          />
+          <TextField
+            value={max}
+            onChange={event => {
+              setMax(event.target.value)
+            }}
+            placeholder="Enter max score"
+          />
+
+          <Button
+            variant="contained"
+            color="primary"
+            type="submit"
+            style={{ marginLeft: 20 }}
+            disabled={!ok}
+            onClick={() => {
+              model.setMinScore(
+                min !== '' && !Number.isNaN(+min) ? +min : undefined,
+              )
+              model.setMaxScore(
+                max !== '' && !Number.isNaN(+max) ? +max : undefined,
+              )
+              handleClose()
+            }}
+          >
+            Submit
+          </Button>
+        </div>
+      </DialogContent>
+    </Dialog>
+  )
+}

package/src/MultiLinearWiggleDisplay/components/Tooltip.tsx

@@ -0,0 +1,76 @@
+import React from 'react'
+import { observer } from 'mobx-react'
+import { Feature } from '@jbrowse/core/util'
+
+// locals
+import { Source, toP } from '../../util'
+import Tooltip, { TooltipContentsComponent } from '../../Tooltip'
+
+const en = (n: number) => n.toLocaleString('en-US')
+
+const TooltipContents = React.forwardRef<
+  HTMLDivElement,
+  { model: { sources: Source[] }; feature: Feature }
+>(({ model, feature }, ref) => {
+  const start = feature.get('start')
+  const end = feature.get('end')
+  const refName = feature.get('refName')
+  const coord = start === end ? en(start) : `${en(start)}..${en(end)}`
+  const sources = feature.get('sources') as Record<string, { score: number }>
+  const source = feature.get('source')
+  const summary = feature.get('summary')
+  const obj = Object.fromEntries(model.sources.map(ent => [ent.name, ent]))
+
+  return (
+    <div ref={ref}>
+      {[refName, coord].filter(f => !!f).join(':')}
+      <br />
+      {sources ? (
+        <table>
+          <thead>
+            <tr>
+              <th>color</th>
+              <th>source</th>
+              <th>score</th>
+            </tr>
+          </thead>
+          <tbody>
+            {Object.entries(sources).map(([source, data]) => (
+              <tr key={source}>
+                <td style={{ background: obj[source]?.color }}> </td>
+                <td>{source}</td>
+                <td>{toP(data.score)}</td>
+              </tr>
+            ))}
+          </tbody>
+        </table>
+      ) : (
+        <span>
+          {source}{' '}
+          {summary
+            ? `min:${toP(feature.get('minScore'))} avg:${toP(
+                feature.get('score'),
+              )} max:${toP(feature.get('maxScore'))}`
+            : toP(feature.get('score'))}
+        </span>
+      )}
+    </div>
+  )
+})
+
+type Coord = [number, number]
+
+const WiggleTooltip = observer(
+  (props: {
+    model: { featureUnderMouse: Feature; sources: Source[]; rowHeight: number }
+    height: number
+    offsetMouseCoord: Coord
+    clientMouseCoord: Coord
+    clientRect?: DOMRect
+    TooltipContents?: TooltipContentsComponent
+  }) => {
+    return <Tooltip useClientY TooltipContents={TooltipContents} {...props} />
+  },
+)
+export default WiggleTooltip
+export { Tooltip }