settings.js

/**
 * Created by Florin Chelaru ( florinc [at] umd [dot] edu )
 * Date: 10/9/13
 * Time: 11:13 AM
 */

/**
 * Overrides the default configuration settings for EpiViz
 */
epiviz.EpiViz.SETTINGS = {

  // PHP/MySQL Data

  dataServerLocation: 'http://epiviz.cbcb.umd.edu/data/', // TODO: Fill in

  chartSaverLocation: 'src/chart_saving/save_svg.php',

  // Navigation settings

  zoominRatio: 0.8,
  zoomoutRatio: 1.2,
  navigationStepRatio: 0.2,

  navigationDelay: 100,

  // Initial genome location

  seqName: 'chr11',
  startLocation: 99800000,
  endLocation: 103383180,

  // Plug-ins

  dataProviders: [
    sprintf('epiviz.data.WebServerDataProvider,%s,%s',
      epiviz.data.WebServerDataProvider.DEFAULT_ID,
      'http://epiviz.cbcb.umd.edu/data/main.php'),
    sprintf('epiviz.data.WebServerDataProvider,%s,%s',
      'mei-id',
      'http://localhost/epiviz-data-github/main.php')
  ],

  workspacesDataProvider: sprintf('epiviz.data.WebServerDataProvider,%s,%s',
    'workspaces_provider',
    'http://epiviz.cbcb.umd.edu/data/main.php'), // TODO: Fill in

  cacheUpdateIntervalMilliseconds: 30000,

  chartTypes: [
    'epiviz.plugins.charts.BlocksTrackType',
    'epiviz.plugins.charts.LineTrackType',
    'epiviz.plugins.charts.ScatterPlotType',
    'epiviz.plugins.charts.GenesTrackType',
    'epiviz.plugins.charts.HeatmapPlotType'
  ],

  // Chart default settings

  chartSettings: {
    plot: {
      width: 400,
      height: 400,
      margins: new epiviz.ui.charts.Margins(15, 30, 30, 15),
      colors: new epiviz.ui.charts.ColorPalette(epiviz.Config.COLORS_BRIGHT)
    },

    track: {
      width: '100%',
      height: 90,
      margins: new epiviz.ui.charts.Margins(25, 20, 23, 10),
      colors: new epiviz.ui.charts.ColorPalette(epiviz.Config.COLORS_BRIGHT)
    },

    'epiviz.plugins.charts.GenesTrack': {
      height: 120,
      colors: new epiviz.ui.charts.ColorPalette([epiviz.Config.COLORS_MEDIUM[0], epiviz.Config.COLORS_MEDIUM[0], epiviz.Config.COLORS_MEDIUM[2], epiviz.Config.COLORS_MEDIUM[1], epiviz.Config.COLORS_MEDIUM[3], epiviz.Config.COLORS_MEDIUM[6], epiviz.Config.COLORS_MEDIUM[7]])
    },

    'epiviz.plugins.charts.ScatterPlot': {
      margins: new epiviz.ui.charts.Margins(15, 50, 50, 15)
    },

    'epiviz.plugins.charts.HeatmapPlot': {
      width: 800,
      height: 400,
      margins: new epiviz.ui.charts.Margins(80, 120, 40, 40),
      colors: new epiviz.ui.charts.ColorPalette(['#ffffff'].concat(epiviz.Config.COLORS_BRIGHT))
    }

  },

  chartCustomSettings: {
    'epiviz.plugins.charts.BlocksTrack': {
      minBlockDistance: 3
    },
    'epiviz.plugins.charts.GenesTrack': {

    },
    'epiviz.plugins.charts.LineTrack': {
      maxPoints: 100,
      showPoints: true,
      showLines: true,
      pointRadius: 3,
      lineThickness: 2
    },
    'epiviz.plugins.charts.ScatterPlot': {
      circleRadiusRatio: 0.01
    },
    'epiviz.plugins.charts.HeatmapPlot': {
      label: 'probe',
      maxColumns: 40
    }
  },

  defaultWorkspaceSettings: {
    name: epiviz.workspaces.Workspace.DEFAULT_WORKSPACE_NAME,
    content: {
      range: {
        seqName: 'chr11',
        start: 99800000,
        width: 3583180
      },
      measurements: [
        {
          id: 'genes',
          name: 'Genes',
          type: 'range',
          datasourceId: 'genes',
          datasourceGroup: 'genes',
          dataprovider: epiviz.data.WebServerDataProvider.DEFAULT_ID,
          formula: null,
          defaultChartType: 'Genes Track',
          annotation: null,
          minValue: null,
          maxValue: null,
          metadata: ['gene', 'entrez', 'exon_starts', 'exon_ends']
        }
      ],
      charts: {
        track: [
          {
            id: 'track-genes-initial',
            type: 'epiviz.plugins.charts.GenesTrack',
            properties: { width: 837, height: 120,
              margins: { top: 25, left: 20, bottom: 23, right: 10 },
              measurements: [0],
              colors: [epiviz.Config.COLORS_MEDIUM[4], epiviz.Config.COLORS_MEDIUM[0], epiviz.Config.COLORS_MEDIUM[2], epiviz.Config.COLORS_MEDIUM[1]],
              customSettings: {}
            }
          }
        ],
        plot: []
      }
    }
  }
};