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florin-chelaru/my-demo-settings.js

Created September 30, 2015 16:23
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my-demo-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.Config.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: 0,
// Plug-ins
dataProviders: [
sprintf('epiviz.data.WebServerDataProvider,%s,%s',
epiviz.Config.DEFAULT_DATA_PROVIDER_ID,
'http://epiviz.cbcb.umd.edu/data/main.php') // TODO: Fill in
],
workspacesDataProvider: sprintf('epiviz.data.WebServerDataProvider,%s,%s',
'workspaces_provider',
'http://epiviz.cbcb.umd.edu/data/main.php'), // TODO: Fill in
cacheUpdateIntervalMilliseconds: 30000,
maxSearchResults: 12,
chartTypes: [
'epiviz.plugins.charts.BlocksTrackType',
'epiviz.plugins.charts.LineTrackType',
'epiviz.plugins.charts.StackedLineTrackType',
'epiviz.plugins.charts.ScatterPlotType',
'epiviz.plugins.charts.GenesTrackType',
'epiviz.plugins.charts.HeatmapPlotType',
'epiviz.plugins.charts.LinePlotType',
'epiviz.plugins.charts.StackedLinePlotType'
],
// Chart default settings
chartSettings: {
default: {
colors: 'd3-category10',
decorations: [
'epiviz.ui.charts.decoration.RemoveChartButton',
'epiviz.ui.charts.decoration.SaveChartButton',
'epiviz.ui.charts.decoration.CustomSettingsButton',
'epiviz.ui.charts.decoration.EditCodeButton',
'epiviz.ui.charts.decoration.ChartColorsButton',
'epiviz.ui.charts.decoration.ChartLoaderAnimation',
'epiviz.ui.charts.decoration.ChartResize'
]
},
plot: {
width: 400,
height: 400,
margins: new epiviz.ui.charts.Margins(15, 30, 30, 15),
decorations: [
'epiviz.ui.charts.decoration.ToggleTooltipButton',
'epiviz.ui.charts.decoration.ChartTooltip',
'epiviz.ui.charts.decoration.ChartFilterCodeButton'
]
},
track: {
width: '100%',
height: 90,
margins: new epiviz.ui.charts.Margins(25, 20, 23, 10),
decorations: [
'epiviz.ui.charts.decoration.ToggleTooltipButton',
'epiviz.ui.charts.decoration.ChartTooltip',
'epiviz.ui.charts.decoration.ChartFilterCodeButton'
]
},
'epiviz.plugins.charts.GenesTrack': {
height: 120,
colors: 'genes-default'
},
'epiviz.plugins.charts.LineTrack': {
decorations: [
'epiviz.ui.charts.decoration.ChartGroupByMeasurementsCodeButton',
'epiviz.ui.charts.decoration.ChartColorByMeasurementsCodeButton'
]
},
'epiviz.plugins.charts.StackedLineTrack': {
height: 300
},
'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),
decorations: [
'epiviz.ui.charts.decoration.ChartGroupByMeasurementsCodeButton',
'epiviz.ui.charts.decoration.ChartOrderByMeasurementsCodeButton',
'epiviz.ui.charts.decoration.ChartColorByRowCodeButton'
],
colors: 'heatmap-default'
},
'epiviz.plugins.charts.LinePlot': {
width: 800,
height: 400,
margins: new epiviz.ui.charts.Margins(30, 30, 50, 15),
decorations: [
'epiviz.ui.charts.decoration.ChartGroupByMeasurementsCodeButton',
'epiviz.ui.charts.decoration.ChartColorByRowCodeButton',
'epiviz.ui.charts.decoration.ChartOrderByMeasurementsCodeButton'
],
colors: 'd3-category20b'
},
'epiviz.plugins.charts.StackedLinePlot': {
width: 800,
height: 400,
margins: new epiviz.ui.charts.Margins(30, 30, 50, 15),
decorations: [
'epiviz.ui.charts.decoration.ChartGroupByMeasurementsCodeButton',
'epiviz.ui.charts.decoration.ChartColorByRowCodeButton',
'epiviz.ui.charts.decoration.ChartOrderByMeasurementsCodeButton'
],
colors: 'd3-category20b'
}
},
chartCustomSettings: {
'epiviz.plugins.charts.BlocksTrack': {
minBlockDistance: 3
},
'epiviz.plugins.charts.GenesTrack': {
},
'epiviz.plugins.charts.LineTrack': {
step: 150,
showPoints: true,
showLines: true,
pointRadius: 3,
lineThickness: 2
},
'epiviz.plugins.charts.ScatterPlot': {
circleRadiusRatio: 0.01
},
'epiviz.plugins.charts.HeatmapPlot': {
maxColumns: 120
}
},
defaultWorkspaceSettings: {
name: epiviz.Config.DEFAULT_WORKSPACE_NAME,
content: {
range: {
seqName: 'chr11',
start: 99800000,
width: 3583180
},
measurements: [
{
id: 'genes',
name: 'Genes',
type: 'range',
datasourceId: 'genes',
datasourceGroup: 'genes',
dataprovider: epiviz.Config.DEFAULT_DATA_PROVIDER_ID,
formula: null,
defaultChartType: 'Genes Track',
annotation: null,
minValue: null,
maxValue: null,
metadata: ['gene', 'entrez', 'exon_starts', 'exon_ends']
}
],
charts: {
track: [
],
plot: []
}
}
},
clustering: {
algorithms: [
'epiviz.ui.charts.transform.clustering.NoneClustering',
'epiviz.ui.charts.transform.clustering.AgglomerativeClustering'
],
metrics: ['epiviz.ui.charts.transform.clustering.EuclideanMetric'],
linkages: ['epiviz.ui.charts.transform.clustering.CompleteLinkage']
},
colorPalettes: [
new epiviz.ui.charts.ColorPalette(
['#025167', '#e7003e', '#ffcd00', '#057d9f', '#970026', '#ffe373', '#ff8100'],
'Epiviz v1.0 Colors', 'epiviz-v1'),
new epiviz.ui.charts.ColorPalette(
['#1859a9', '#ed2d2e', '#008c47', '#010101', '#f37d22', '#662c91', '#a11d20', '#b33893'],
'Epiviz v2.0 Bright', 'epiviz-v2-bright'),
new epiviz.ui.charts.ColorPalette(
['#b8d2eb', '#f2aeac', '#d8e4aa', '#cccccc', '#f2d1b0', '#d4b2d3', '#ddb8a9', '#ebbfd9'],
'Epiviz v2.0 Light', 'epiviz-v2-light'),
new epiviz.ui.charts.ColorPalette(
['#599ad3', '#f1595f', '#79c36a', '#727272', '#f9a65a', '#9e66ab', '#cd7058', '#d77fb3'],
'Epiviz v2.0 Medium', 'epiviz-v2-medium'),
new epiviz.ui.charts.ColorPalette(
["#1f77b4", "#ff7f0e", "#2ca02c", "#d62728", "#9467bd", "#8c564b", "#e377c2", "#7f7f7f", "#bcbd22", "#17becf"],
'D3 Category 10', 'd3-category10'),
new epiviz.ui.charts.ColorPalette(
["#1f77b4", "#aec7e8", "#ff7f0e", "#ffbb78", "#2ca02c", "#98df8a", "#d62728", "#ff9896", "#9467bd", "#c5b0d5", "#8c564b", "#c49c94", "#e377c2", "#f7b6d2", "#7f7f7f", "#c7c7c7", "#bcbd22", "#dbdb8d", "#17becf", "#9edae5"],
'D3 Category 20', 'd3-category20'),
new epiviz.ui.charts.ColorPalette(
["#393b79", "#5254a3", "#6b6ecf", "#9c9ede", "#637939", "#8ca252", "#b5cf6b", "#cedb9c", "#8c6d31", "#bd9e39", "#e7ba52", "#e7cb94", "#843c39", "#ad494a", "#d6616b", "#e7969c", "#7b4173", "#a55194", "#ce6dbd", "#de9ed6"],
'D3 Category 20b', 'd3-category20b'),
new epiviz.ui.charts.ColorPalette(
["#3182bd", "#6baed6", "#9ecae1", "#c6dbef", "#e6550d", "#fd8d3c", "#fdae6b", "#fdd0a2", "#31a354", "#74c476", "#a1d99b", "#c7e9c0", "#756bb1", "#9e9ac8", "#bcbddc", "#dadaeb", "#636363", "#969696", "#bdbdbd", "#d9d9d9"],
'D3 Category 20c', 'd3-category20c'),
new epiviz.ui.charts.ColorPalette(
['#f9a65a', '#599ad3', '#79c36a', '#f1595f', '#727272', '#cd7058', '#d77fb3'],
'Genes Default', 'genes-default'),
new epiviz.ui.charts.ColorPalette(
['#1859a9', '#ed2d2e', '#008c47', '#010101', '#f37d22', '#662c91', '#a11d20', '#b33893'],
'Heatmap Default', 'heatmap-default')
]
};
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