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Circster: add config options for min/max values and color.

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This commit is contained in:
Jeremy Goecks
2014-06-26 10:56:05 -04:00
parent c6c6be08f4
commit dc20caec65
4 changed files with 82 additions and 27 deletions
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static/scripts/packed/viz/circster.js
+1 -1
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static/scripts/packed/viz/visualization.js
+1 -1
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static/scripts/viz/circster.js
+77 -24
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@@ -1,7 +1,15 @@
define(["utils/utils", "libs/underscore", "libs/d3", "viz/visualization", "utils/config"], function(utils, _, d3, visualization, config) {
// load required libraries
require(
[
'utils/utils',
'libs/farbtastic',
], function(mod_utils)
{
// load css
mod_utils.cssLoadFile("static/style/circster.css");
});
// Load needed CSS.
utils.cssLoadFile("static/style/circster.css");
define(["libs/underscore", "libs/d3", "viz/visualization", "utils/config"], function(_, d3, visualization, config) {
/**
* Utility class for working with SVG.
@@ -72,14 +80,14 @@ var UsesTicks = {
.attr("y1", tick_coords[3])
.style("stroke", "#000");
ticks.append("text")
.attr("x", text_coords[0])
.attr("y", text_coords[1])
.attr("dx", text_coords[2])
.attr("dy", text_coords[3])
.attr("text-anchor", text_anchor)
.attr("transform", textTransform)
.text(function(d) { return d.label; });
return ticks.append("text")
.attr("x", text_coords[0])
.attr("y", text_coords[1])
.attr("dx", text_coords[2])
.attr("dy", text_coords[3])
.attr("text-anchor", text_anchor)
.attr("transform", textTransform)
.text(function(d) { return d.label; });
},
/**
@@ -572,11 +580,13 @@ var CircsterTrackView = Backbone.View.extend({
return rval;
}), function(p_data) { return p_data === null; } );
// Transition each path.
// Transition each path for data and color.
var color = track.get('config').get_value('color');
chrom_data_paths.each(function(path, index) {
d3.select(this).transition().duration(1000).attr('d', path_data[index]);
d3.select(this).transition().duration(1000)
.style('stroke', color).style('fill', color)
.attr('d', path_data[index]);
});
});
}
},
@@ -587,16 +597,14 @@ var CircsterTrackView = Backbone.View.extend({
_transition_labels: function() {},
/**
* Update data bounds.
* Update data bounds. If there are new_bounds, use them; otherwise use
* default data bounds.
*/
_update_data_bounds: function() {
_update_data_bounds: function(new_bounds) {
var old_bounds = this.data_bounds;
this.data_bounds = this.get_data_bounds(this.track.get('data_manager').get_genome_wide_data(this.genome));
// If bounds have changed, transition all paths to use the new data bounds.
if (this.data_bounds[0] < old_bounds[0] || this.data_bounds[1] > old_bounds[1]) {
this._transition_chrom_data();
}
this.data_bounds = new_bounds ||
this.get_data_bounds(this.track.get('data_manager').get_genome_wide_data(this.genome));
this._transition_chrom_data();
},
/**
@@ -612,6 +620,8 @@ var CircsterTrackView = Backbone.View.extend({
$.when(track.get('data_manager').get_genome_wide_data(this.genome)).then(function(genome_wide_data) {
// Set bounds.
self.data_bounds = self.get_data_bounds(genome_wide_data);
track.get('config').set_value('min_value', self.data_bounds[0]);
track.get('config').set_value('max_value', self.data_bounds[1]);
// Merge chroms layout with data.
layout_and_data = _.zip(chrom_arcs, genome_wide_data),
@@ -746,6 +756,31 @@ _.extend(CircsterChromLabelTrackView.prototype, UsesTicks);
*/
var CircsterQuantitativeTrackView = CircsterTrackView.extend({
initialize: function(options) {
CircsterTrackView.prototype.initialize.call(this, options);
// When config settings change, update view.
var track_config = this.track.get('config');
track_config.get('min_value').on('change:value', this._update_min_max, this);
track_config.get('max_value').on('change:value', this._update_min_max, this);
track_config.get('color').on('change:value', this._transition_chrom_data, this);
},
/**
* Update track when min and/or max are changed.
*/
_update_min_max: function() {
var track_config = this.track.get('config'),
new_bounds = [track_config.get_value('min_value'), track_config.get_value('max_value')];
this._update_data_bounds(new_bounds);
// FIXME: this works to update tick/text bounds, but there's probably a better way to do this
// by updating the data itself.
this.parent_elt.selectAll('.min_max').text(function(d, i) {
return new_bounds[i];
});
},
/**
* Returns quantile for an array of numbers.
*/
@@ -816,8 +851,26 @@ var CircsterQuantitativeTrackView = CircsterTrackView.extend({
return "rotate(90)";
};
// FIXME:
// (1) using min_max class below is needed for _update_min_max, which could be improved.
// (2) showing config on tick click should be replaced by proper track config icon.
// Draw min, max on first chrom only.
this.drawTicks(this.parent_elt, [ this.chroms_layout[0] ], this._data_bounds_ticks_fn(), textTransform, true);
var ticks = this.drawTicks(this.parent_elt, [ this.chroms_layout[0] ],
this._data_bounds_ticks_fn(), textTransform, true)
.classed('min_max', true);
// Show config when ticks are clicked on.
_.each(ticks, function(tick) {
$(tick).click(function() {
var view = new config.ConfigSettingCollectionView({
collection: self.track.get('config')
});
view.render_in_modal('Configure Track');
});
});
/*
// Filter for visible chroms, then for every third chrom so that labels attached to only every
@@ -909,7 +962,7 @@ var CircsterBigWigTrackView = CircsterQuantitativeTrackView.extend({
// For max, use 98% quantile in attempt to avoid very large values. However, this max may be 0
// for sparsely populated data, so use max in that case.
return [ _.min(values), this._quantile(values, 0.5) || _.max(values) ];
return [ _.min(values), this._quantile(values, 0.98) || _.max(values) ];
}
});
static/scripts/viz/visualization.js
+3 -1
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@@ -895,7 +895,9 @@ var BackboneTrack = Backbone.Model.extend(CustomToJSON).extend({
// -- Set up config settings. --
var models = [
{ key: 'name', value: this.get('dataset').get('name') },
{ key: 'color' }
{ key: 'color' },
{ key: 'min_value', label: 'Min Value', type: 'float', default_value: 0 },
{ key: 'max_value', label: 'Max Value', type: 'float', default_value: 1 }
];
this.set('config', config_mod.ConfigSettingCollection.from_models_and_saved_values(models, options.prefs));