Files
galaxy/static/scripts/mvc/visualization/scatterplotControlForm.js
T

632 lines
27 KiB
JavaScript

/* =============================================================================
todo:
I'd like to move the svg creation out of the splot constr. to:
allow adding splots to an existing canvas
allow mult. splots sharing a canvas
outside this:
BUG: setting width, height in plot controls doesn't re-interpolate data locations!!
BUG?: get metadata_column_names (from datatype if necessary)
BUG: single vis in popupmenu should have tooltip with that name NOT 'Visualizations'
wire label setters, anim setter
TwoVarScatterplot:
??: maybe better to do this with a canvas...
save as visualization
to seperate file?
remove underscore dependencies
add interface to change values (seperate)?
download svg -> base64 encode
incorporate glyphs, glyph state renderers
ScatterplotSettingsForm:
some css bug that lowers the width of settings form when plot-controls tab is open
causes chart to shift
what can be abstracted/reused for other graphs?
avoid direct manipulation of this.plot
allow option to put plot into seperate tab of interface (for small multiples)
provide callback in view to load data incrementally - for large sets
paginate
handle rerender
use endpoint (here and on the server (fileptr))
fetch (new?) data
handle rerender
use d3.TSV?
render warning on long data (> maxDataPoints)
adjust endpoint
selectable list of preset column comparisons (rnaseq etc.)
how to know what sort of Tabular the data is?
smarter about headers
validate columns selection (here or server)
set stats column names by selected columns
move chart into tabbed area...
Scatterplot.mako:
multiple plots on one page (small multiples)
?? ensure svg styles thru d3 or css?
d3: configable (easily)
css: standard - better maintenance
? override at config
============================================================================= */
/**
* Scatterplot control UI as a backbone view
* handles:
* getting the desired data
* configuring the plot display
* showing (general) statistics
*
* initialize attributes REQUIRES a dataset and an apiDatasetsURL
*/
var ScatterplotControlForm = Backbone.View.extend( LoggableMixin ).extend({
//logger : console,
className : 'scatterplot-control-form',
//NOTE: should include time needed to render
dataLoadDelay : 4000,
dataLoadSize : 5000,
loadingIndicatorImage : 'loading_small_white_bg.gif',
fetchMsg : 'Fetching data...',
renderMsg : 'Rendering...',
initialize : function( attributes ){
this.log( this + '.initialize, attributes:', attributes );
this.dataset = null;
this.chartConfig = null;
this.chart = null;
this.loader = null;
// set up refs to the four tab areas
this.$dataControl = null;
this.$chartControl = null;
this.$statsDisplay = null;
this.$chartDisplay = null;
this.dataFetch = null;
this.initializeFromAttributes( attributes );
this.initializeChart( attributes );
this.initializeDataLoader( attributes );
},
initializeFromAttributes : function( attributes ){
// required settings: ensure certain vars we need are passed in attributes
if( !attributes || !attributes.dataset ){
throw( "ScatterplotView requires a dataset" );
} else {
this.dataset = attributes.dataset;
}
if( jQuery.type( this.dataset.metadata_column_types ) === 'string' ){
this.dataset.metadata_column_types = this.dataset.metadata_column_types.split( ', ' );
}
this.log( '\t dataset:', this.dataset );
// attempt to get possible headers from the data's first line
if( this.dataset.comment_lines && this.dataset.comment_lines.length ){
//TODO:??
var firstLine = this.dataset.comment_lines[0],
possibleHeaders = firstLine.split( '\t' );
if( possibleHeaders.length === this.dataset.metadata_column_types.length ){
this.possibleHeaders = possibleHeaders;
}
}
// passed from mako helper
//TODO: integrate to galaxyPaths
//TODO: ?? seems like data loader section would be better
if( !attributes.apiDatasetsURL ){
throw( "ScatterplotView requires a apiDatasetsURL" );
} else {
this.dataURL = attributes.apiDatasetsURL + '/' + this.dataset.id + '?';
}
this.log( '\t dataURL:', this.dataURL );
},
initializeChart : function( attributes ){
// set up the basic chart infrastructure and config (if any)
this.chartConfig = attributes.chartConfig || {};
//if( this.logger ){ this.chartConfig.debugging = true; }
this.log( '\t initial chartConfig:', this.chartConfig );
this.chart = new TwoVarScatterplot( this.chartConfig );
//TODO: remove 2nd ref, use this.chart.config
this.chartConfig = this.chart.config;
},
initializeDataLoader : function( attributes ){
// set up data loader
var view = this;
this.loader = new LazyDataLoader({
//logger : ( this.logger )?( this.logger ):( null ),
// we'll generate this when columns are chosen
url : null,
start : attributes.start || 0,
//NOTE: metadata_data_lines can be null (so we won't know the total)
total : attributes.total || this.dataset.metadata_data_lines,
delay : this.dataLoadDelay,
size : this.dataLoadSize,
buildUrl : function( start, size ){
// currently VERY SPECIFIC to using data_providers.py start_val, max_vals params
return this.url + '&' + jQuery.param({
start_val: start,
max_vals: size
});
}
});
$( this.loader ).bind( 'error', function( event, status, error ){
view.log( 'ERROR:', status, error );
alert( 'ERROR fetching data:\n' + status + '\n' + error );
view.hideLoadingIndicator();
});
},
// ------------------------------------------------------------------------- CONTROLS RENDERING
render : function(){
this.log( this + '.render' );
// render the tab controls, areas and loading indicator
this.$el.append( ScatterplotControlForm.templates.mainLayout({
loadingIndicatorImagePath : galaxy_config.root + 'static/images/' + this.loadingIndicatorImage,
message : ''
}));
// render the tab content
this.$dataControl = this._render_dataControl();
this.$chartControl = this._render_chartControl();
this.$statsDisplay = this.$el.find( '.tab-pane#stats-display' );
this.$chartDisplay = this._render_chartDisplay();
// auto render if given both x, y column choices in query for page
//TODO:?? add autoRender=1 to query maybe?
if( this.chartConfig.xColumn && this.chartConfig.yColumn ){
this.renderChart();
}
// set up behaviours
this.$el.find( '[title]' ).tooltip();
// uncomment any of the following to have that tab show on initial load (for testing)
//this.$el.find( 'ul.nav' ).find( 'a[href="#data-control"]' ).tab( 'show' );
//this.$el.find( 'ul.nav' ).find( 'a[href="#chart-control"]' ).tab( 'show' );
//this.$el.find( 'ul.nav' ).find( 'a[href="#stats-display"]' ).tab( 'show' );
//this.$el.find( 'ul.nav' ).find( 'a[href="#chart-display"]' ).tab( 'show' );
return this;
},
_render_dataControl : function(){
// controls for which columns are used to plot datapoints (and ids/additional info to attach if desired)
var view = this,
allColumns = [],
numericColumns = [],
usePossibleHeaders = ( this.possibleHeaders && this.$dataControl )?
( this.$dataControl.find( '#first-line-header-checkbox' ).is( ':checked' ) ):( false );
// gather column indeces (from metadata_column_types) and names (from metadata_columnnames)
_.each( this.dataset.metadata_column_types, function( type, index ){
// use a 1 based index in names/values within the form (will be dec. when parsed out)
var oneBasedIndex = index + 1,
// default name is 'column <index>'...
name = 'column ' + oneBasedIndex;
// ...but label with the name if available...
if( view.dataset.metadata_column_names ){
name = view.dataset.metadata_column_names[ index ];
// ...or, use the first line as headers if the user wants
} else if( usePossibleHeaders ){
name = view.possibleHeaders[ index ];
}
// cache all columns here
allColumns.push({ index: oneBasedIndex, name: name });
// filter numeric columns to their own list
if( type === 'int' || type === 'float' ){
numericColumns.push({ index: oneBasedIndex, name: name });
}
});
//TODO: other vals: max_vals, start_val, pagination (chart-settings)
// render the html
var $dataControl = this.$el.find( '.tab-pane#data-control' );
$dataControl.html( ScatterplotControlForm.templates.dataControl({
allColumns : allColumns,
numericColumns : numericColumns,
possibleHeaders : ( this.possibleHeaders )?( this.possibleHeaders.join( ', ' ) ):( '' ),
usePossibleHeaders : usePossibleHeaders
}));
if( !this.dataset.metadata_column_names && this.possibleHeaders ){
$dataControl.find( '#first-line-header' ).show();
}
// preset to column selectors if they were passed in the config in the query string
$dataControl.find( '#X-select' ).val( this.chartConfig.xColumn );
$dataControl.find( '#Y-select' ).val( this.chartConfig.yColumn );
if( this.chartConfig.idColumn !== undefined ){
$dataControl.find( '#include-id-checkbox' )
.attr( 'checked', true ).trigger( 'change' );
$dataControl.find( '#ID-select' ).val( this.chartConfig.idColumn );
}
return $dataControl;
},
_render_chartControl : function(){
// tab content to control how the chart is rendered (data glyph size, chart size, etc.)
var view = this,
$chartControl = this.$el.find( '.tab-pane#chart-control' ),
// limits for controls (by control/chartConfig id)
//TODO: move into TwoVarScatterplot
controlRanges = {
'datapointSize' : { min: 2, max: 10, step: 1 },
'width' : { min: 200, max: 800, step: 20 },
'height' : { min: 200, max: 800, step: 20 }
};
// render the html
$chartControl.append( ScatterplotControlForm.templates.chartControl( this.chartConfig ) );
// set up behaviours, js on sliders
$chartControl.find( '.numeric-slider-input' ).each( function(){
var $this = $( this ),
$output = $this.find( '.slider-output' ),
$slider = $this.find( '.slider' ),
id = $this.attr( 'id' );
//chartControl.log( 'slider set up', 'this:', $this, 'slider:', $slider, 'id', id );
// what to do when the slider changes: update display and update chartConfig
//TODO: move out of loop
function onSliderChange(){
var $this = $( this ),
newValue = $this.slider( 'value' );
//chartControl.log( 'slider change', 'this:', $this, 'output:', $output, 'value', newValue );
$output.text( newValue );
//chartControl.chartConfig[ id ] = newValue;
}
$slider.slider( _.extend( controlRanges[ id ], {
value : view.chartConfig[ id ],
change : onSliderChange,
slide : onSliderChange
}));
});
return $chartControl;
},
_render_chartDisplay : function(){
// render the tab content where the chart is displayed (but not the chart itself)
var $chartDisplay = this.$el.find( '.tab-pane#chart-display' );
$chartDisplay.append( ScatterplotControlForm.templates.chartDisplay( this.chartConfig ) );
return $chartDisplay;
},
// ------------------------------------------------------------------------- EVENTS
events : {
'change #include-id-checkbox' : 'toggleThirdColumnSelector',
'change #first-line-header-checkbox' : 'rerenderDataControl',
'click #data-control #render-button' : 'renderChart',
'click #chart-control #render-button' : 'changeChartSettings'
},
toggleThirdColumnSelector : function(){
// show/hide the id selector on the data settings panel
this.$el.find( 'select[name="ID"]' ).parent().toggle();
},
rerenderDataControl : function(){
this.$dataControl = this._render_dataControl();
},
showLoadingIndicator : function( message, callback ){
// display the loading indicator over the tab panels if hidden, update message (if passed)
message = message || '';
var indicator = this.$el.find( 'div#loading-indicator' );
messageBox = indicator.find( '.loading-message' );
if( indicator.is( ':visible' ) ){
if( message ){
messageBox.fadeOut( 'fast', function(){
messageBox.text( message );
messageBox.fadeIn( 'fast', callback );
});
} else {
callback();
}
} else {
if( message ){ messageBox.text( message ); }
indicator.fadeIn( 'fast', callback );
}
},
hideLoadingIndicator : function( callback ){
this.$el.find( 'div#loading-indicator' ).fadeOut( 'fast', callback );
},
// ------------------------------------------------------------------------- CHART/STATS RENDERING
renderChart : function(){
// fetch the data, (re-)render the chart
this.log( this + '.renderChart' );
//TODO: separate data fetch
// this is a complete re-render, so clear the prev. data
this.data = null;
this.meta = null;
// update the chartConfig (here and chart) using chart settings
//TODO: separate and improve (used in changeChartSettings too)
_.extend( this.chartConfig, this.getChartSettings() );
this.log( '\t chartConfig:', this.chartConfig );
this.chart.updateConfig( this.chartConfig, false );
// build the url with the current data settings
this.loader.url = this.dataURL + '&' + jQuery.param( this.getDataSettings() );
this.log( '\t loader: total lines:', this.loader.total, ' url:', this.loader.url );
// bind the new data event to: aggregate data, update the chart and stats with new data
var view = this;
$( this.loader ).bind( 'loaded.new', function( event, response ){
view.log( view + ' loaded.new', response );
// aggregate data and meta
view.postProcessDataFetchResponse( response );
view.log( '\t postprocessed data:', view.data );
view.log( '\t postprocessed meta:', view.meta );
// update the chart and stats
view.showLoadingIndicator( view.renderMsg, function(){
view.chart.render( view.data, view.meta );
view.renderStats( view.data, view.meta );
view.hideLoadingIndicator();
});
});
// when all data loaded - unbind (or we'll start doubling event handlers)
$( this.loader ).bind( 'complete', function( event, data ){
view.log( view + ' complete', data );
$( view.loader ).unbind();
});
// begin loading the data, switch to the chart display tab
view.showLoadingIndicator( view.fetchMsg, function(){
view.$el.find( 'ul.nav' ).find( 'a[href="#chart-display"]' ).tab( 'show' );
view.loader.load();
});
},
renderStats : function(){
this.log( this + '.renderStats' );
// render the stats table in the stats panel
//TODO: there's a better way
this.$statsDisplay.html( ScatterplotControlForm.templates.statsDisplay({
stats: [
{ name: 'Count', xval: this.meta[0].count, yval: this.meta[1].count },
{ name: 'Min', xval: this.meta[0].min, yval: this.meta[1].min },
{ name: 'Max', xval: this.meta[0].max, yval: this.meta[1].max },
{ name: 'Sum', xval: this.meta[0].sum, yval: this.meta[1].sum },
{ name: 'Mean', xval: this.meta[0].mean, yval: this.meta[1].mean },
{ name: 'Median', xval: this.meta[0].median, yval: this.meta[1].median }
]
}));
},
changeChartSettings : function(){
// re-render the chart with new chart settings and OLD data
var view = this;
newChartSettings = this.getChartSettings();
// update the chart config from the chartSettings panel controls
_.extend( this.chartConfig, newChartSettings );
this.log( 'this.chartConfig:', this.chartConfig );
this.chart.updateConfig( this.chartConfig, false );
// if there's current data, call chart.render with it (no data fetch)
if( view.data && view.meta ){
view.showLoadingIndicator( view.renderMsg, function(){
view.$el.find( 'ul.nav' ).find( 'a[href="#chart-display"]' ).tab( 'show' );
view.chart.render( view.data, view.meta );
view.hideLoadingIndicator();
});
// no current data, call renderChart instead (which will fetch data)
} else {
this.renderChart();
}
},
// ------------------------------------------------------------------------- DATA AGGREGATION
postProcessDataFetchResponse : function( response ){
// the loader only returns new data - it's up to this to munge the fetches together properly
//TODO: we're now storing data in two places: loader and here
// can't we reduce incoming data into loader.data[0]? are there concurrency problems?
this.postProcessData( response.data );
this.postProcessMeta( response.meta );
},
postProcessData : function( newData ){
// stack the column data on top of each other into this.data
//this.log( this + '.postProcessData:', newData );
var view = this;
// if we already have data: aggregate
if( view.data ){
_.each( newData, function( newColData, colIndex ){
//view.log( colIndex + ' data:', newColData );
//TODO??: time, space efficiency of this?
view.data[ colIndex ] = view.data[ colIndex ].concat( newColData );
});
// otherwise: assign (first load)
} else {
view.data = newData;
}
},
postProcessMeta : function( newMeta ){
// munge the meta data (stats) from the server fetches together
//pre: this.data must be preprocessed (needed for medians)
//this.log( this + '.postProcessMeta:', newMeta );
var view = this,
colTypes = this.dataset.metadata_column_types;
// if we already have meta: aggregate
if( view.meta ){
_.each( newMeta, function( newColMeta, colIndex ){
var colMeta = view.meta[ colIndex ],
colType = colTypes[ colIndex ];
//view.log( '\t ' + colIndex + ' postprocessing meta:', newColMeta );
//view.log( colIndex + ' old meta:',
// 'min:', colMeta.min,
// 'max:', colMeta.max,
// 'sum:', colMeta.sum,
// 'mean:', colMeta.mean,
// 'median:', colMeta.median
//);
//!TODO: at what point are we getting int/float overflow on these?!
//??: need to be null safe?
colMeta.count += ( newColMeta.count )?( newColMeta.count ):( 0 );
//view.log( colIndex, 'count:', colMeta.count );
if( ( colType === 'int' ) || ( colType === 'float' ) ){
//view.log( colIndex + ' incoming meta:',
// 'min:', newColMeta.min,
// 'max:', newColMeta.max,
// 'sum:', newColMeta.sum,
// 'mean:', newColMeta.mean,
// 'median:', newColMeta.median
//);
colMeta.min = Math.min( newColMeta.min, colMeta.min );
colMeta.max = Math.max( newColMeta.max, colMeta.max );
colMeta.sum = newColMeta.sum + colMeta.sum;
colMeta.mean = ( colMeta.count )?( colMeta.sum / colMeta.count ):( null );
// median's a pain bc of sorting (requires the data as well)
var sortedCol = view.data[ colIndex ].slice().sort(),
middleIndex = Math.floor( sortedCol.length / 2 );
if( sortedCol.length % 2 === 0 ){
colMeta.median = ( ( sortedCol[ middleIndex ] + sortedCol[( middleIndex + 1 )] ) / 2 );
} else {
colMeta.median = sortedCol[ middleIndex ];
}
//view.log( colIndex + ' new meta:',
// 'min:', colMeta.min,
// 'max:', colMeta.max,
// 'sum:', colMeta.sum,
// 'mean:', colMeta.mean,
// 'median:', colMeta.median
//);
}
});
// otherwise: assign (first load)
} else {
view.meta = newMeta;
//view.log( '\t meta (first load):', view.meta );
}
},
// ------------------------------------------------------------------------- GET DATA/CHART SETTINGS
getDataSettings : function(){
// parse the column values for both indeces (for the data fetch) and names (for the chart)
var columnSelections = this.getColumnSelections(),
columns = [];
this.log( '\t columnSelections:', columnSelections );
//TODO: validate columns - minimally: we can assume either set by selectors or via a good query string
// get column indices for params, include the desired ID column (if any)
//NOTE: these are presented in human-readable 1 base index (to match the data.peek) - adjust
columns = [
columnSelections.X.colIndex - 1,
columnSelections.Y.colIndex - 1
];
if( this.$dataControl.find( '#include-id-checkbox' ).attr( 'checked' ) ){
columns.push( columnSelections.ID.colIndex - 1 );
}
//TODO: other vals: max, start, page
var params = {
data_type : 'raw_data',
provider : 'column_with_stats',
columns : '[' + columns + ']'
};
this.log( '\t data settings (url params):', params );
return params;
},
getColumnSelections : function(){
// gets the current user-selected values for which columns to fetch from the data settings panel
// returns a map: { column-select name (eg. X) : { colIndex : column-selector val,
// colName : selected option text }, ... }
var selections = {};
this.$dataControl.find( 'div.column-select select' ).each( function(){
var $this = $( this ),
val = $this.val();
selections[ $this.attr( 'name' ) ] = {
colIndex : val,
colName : $this.children( '[value="' + val + '"]' ).text()
};
});
return selections;
},
getChartSettings : function(){
// gets the user-selected chartConfig from the chart settings panel
var settings = {},
colSelections = this.getColumnSelections();
//this.log( 'colSelections:', colSelections );
//TODO: simplify with keys and loop
settings.datapointSize = this.$chartControl.find( '#datapointSize.numeric-slider-input' )
.find( '.slider' ).slider( 'value' );
settings.width = this.$chartControl.find( '#width.numeric-slider-input' )
.find( '.slider' ).slider( 'value' );
settings.height = this.$chartControl.find( '#height.numeric-slider-input' )
.find( '.slider' ).slider( 'value' );
// update axes labels using chartSettings inputs (if not at defaults), otherwise the selects' colName
//TODO: a little confusing
var chartSettingsXLabel = this.$chartControl.find( 'input#X-axis-label' ).val(),
chartSettingsYLabel = this.$chartControl.find( 'input#Y-axis-label' ).val();
settings.xLabel = ( chartSettingsXLabel === 'X' )?
( colSelections.X.colName ):( chartSettingsXLabel );
settings.yLabel = ( chartSettingsYLabel === 'Y' )?
( colSelections.Y.colName ):( chartSettingsYLabel );
settings.animDuration = ( this.$chartControl.find( '#animate-chart' ).is( ':checked' ) )?
( this.chart.defaults.animDuration ):( 0 );
this.log( '\t chartSettings:', settings );
return settings;
},
toString : function(){
return 'ScatterplotControlForm(' + (( this.dataset )?( this.dataset.id ):( '' )) + ')';
}
});
ScatterplotControlForm.templates = {
mainLayout : Handlebars.templates[ 'template-visualization-scatterplotControlForm' ],
dataControl : Handlebars.templates[ 'template-visualization-dataControl' ],
chartControl : Handlebars.templates[ 'template-visualization-chartControl' ],
statsDisplay : Handlebars.templates[ 'template-visualization-statsDisplay' ],
chartDisplay : Handlebars.templates[ 'template-visualization-chartDisplay' ]
};
//==============================================================================