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Trackster: add histogram mode to feature tracks so that user can generate coverage histogram at any level of data. Refactor overlap computation out of modules for now since it's a general purpose method used in multiple modules.

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This commit is contained in:
Jeremy Goecks
2011-04-12 14:40:59 -04:00
parent 7a03b066e7
commit c967bfa36d
1 changed files with 160 additions and 49 deletions
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static/scripts/trackster.js
+160 -49
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@@ -14,6 +14,50 @@ var extend = function() {
return target;
};
/**
* Compute the type of overlap between two regions. They are assumed to be on the same chrom/contig.
* The overlap is computed relative to the second region; hence, OVERLAP_START indicates that the first
* region overlaps the start (but not the end) of the second region.
*/
var BEFORE = 1001, CONTAINS = 1002, OVERLAP_START = 1003, OVERLAP_END = 1004, CONTAINED_BY = 1005, AFTER = 1006;
var compute_overlap = function(first_region, second_region) {
var
first_start = first_region[0], first_end = first_region[1],
second_start = second_region[0], second_end = second_region[1],
overlap;
if (first_start < second_start) {
if (first_end < second_start) {
overlap = BEFORE;
}
else if (first_end <= second_end) {
overlap = OVERLAP_START;
}
else { // first_end > second_end
overlap = CONTAINS;
}
}
else { // first_start >= second_start
if (first_start > second_end) {
overlap = AFTER;
}
else if (first_end <= second_end) {
overlap = CONTAINED_BY;
}
else {
overlap = OVERLAP_END;
}
}
return overlap;
};
/**
* Returns true if regions overlap.
*/
var is_overlap = function(first_region, second_region) {
var overlap = compute_overlap(first_region, second_region);
return (overlap !== BEFORE && overlap !== AFTER);
};
// Encapsulate -- anything to be availabe outside this block is added to exports
var trackster_module = function(require, exports){
@@ -98,7 +142,7 @@ var sortable = function( element, handle ) {
$(this).insertBefore( children.get( i ) );
}
});
}
};
/**
* Calculates step for slider with a given min, max.
@@ -106,7 +150,7 @@ var sortable = function( element, handle ) {
var get_slider_step = function(min, max) {
var range = max - min;
return (range <= 2 ? 0.01 : (range <= 100 ? 1 : (range <= 1000 ? 5 : 10)));
}
};
/**
* Init constants & functions used throughout trackster.
@@ -142,7 +186,7 @@ var
function round_1000(num) {
return Math.round(num * 1000) / 1000;
}
};
/**
* Generic cache that handles key/value pairs.
@@ -2061,14 +2105,14 @@ extend(LineTrack.prototype, TiledTrack.prototype, {
}
});
var FeatureTrack = function (name, view, hda_ldda, dataset_id, prefs, filters, tool, parent_track) {
var FeatureTrack = function(name, view, hda_ldda, dataset_id, prefs, filters, tool, parent_track) {
//
// Preinitialization: do things that need to be done before calling Track and TiledTrack
// initialization code.
//
var track = this;
this.track_type = "FeatureTrack";
this.display_modes = ["Auto", "Dense", "Squish", "Pack"];
this.display_modes = ["Auto", "Histogram", "Dense", "Squish", "Pack"];
// Define and restore track configuration.
this.track_config = new TrackConfig( {
track: this,
@@ -2142,6 +2186,84 @@ extend(FeatureTrack.prototype, TiledTrack.prototype, {
return inc_slots.slot_features( features );
},
/**
* Given feature data, returns summary tree data. Feature data must be sorted by start
* position. Return value is a dict with keys 'data', 'delta' (bin size) and 'max.' Data
* is a two-item list; first item is bin start, second is bin's count.
*/
get_summary_tree_data: function(data, low, high, bin_size) {
var num_bins = Math.floor((high - low)/bin_size),
bins = [],
max_count = 0;
/*
// For debugging:
for (var i = 0; i < data.length; i++)
console.log("\t", data[i][1], data[i][2], data[i][3]);
*/
//
// Loop through bins, counting data for each interval.
//
var data_index_start = 0,
data_index = 0,
data_interval,
bin_index = 0,
bin_interval = [],
cur_bin,
overlap;
// Set bin interval.
var set_bin_interval = function(interval, low, bin_index, bin_size) {
interval[0] = low + bin_index * bin_size;
interval[1] = low + (bin_index + 1) * bin_size;
};
// Loop through bins, data to compute bin counts. Only compute bin counts as long
// as there is data.
while (bin_index < num_bins && data_index_start !== data.length) {
// Find next bin that has data.
var bin_has_data = false;
for (; bin_index < num_bins && !bin_has_data; bin_index++) {
set_bin_interval(bin_interval, low, bin_index, bin_size);
// Loop through data and break if data found that goes in bin.
for (data_index = data_index_start; data_index < data.length; data_index++) {
data_interval = data[data_index].slice(1, 3);
if (is_overlap(data_interval, bin_interval)) {
bin_has_data = true;
break;
}
}
// Break from bin loop if this bin has data.
if (bin_has_data) {
break;
}
}
// Set start index to current data, which is the first to overlap with this bin
// and perhaps with later bins.
data_start_index = data_index;
// Count intervals that overlap with bin.
bins[bins.length] = cur_bin = [bin_interval[0], 0];
for (; data_index < data.length; data_index++) {
data_interval = data[data_index].slice(1, 3);
if (is_overlap(data_interval, bin_interval)) {
cur_bin[1]++;
}
else { break; }
}
// Update max count.
if (cur_bin[1] > max_count) {
max_count = cur_bin[1];
}
// Go to next bin.
bin_index++;
}
return {max: max_count, delta: bin_size, data: bins};
},
/**
* Draw FeatureTrack tile.
*/
@@ -2156,7 +2278,7 @@ extend(FeatureTrack.prototype, TiledTrack.prototype, {
left_offset = this.left_offset,
slots,
required_height;
// Set display mode if Auto.
if (mode === "Auto") {
if (result.dataset_type === "summary_tree") {
@@ -2211,6 +2333,35 @@ extend(FeatureTrack.prototype, TiledTrack.prototype, {
// Canvas element is returned
return canvas;
}
// Drawing coverage histogram. This is different from summary tree because data can feature
// details, but user has requested a histogram.
if (mode === "Histogram") {
// Set height of parent_element
required_height = this.summary_draw_height;
parent_element.parent().css("height", Math.max(this.height_px, required_height) + "px");
// Add label to container div showing maximum count
// TODO: this shouldn't be done at the tile level
this.container_div.find(".yaxislabel").remove();
var max_label = $("<div />").addClass('yaxislabel');
max_label.text( result.max );
max_label.css({ position: "absolute", top: "22px", left: "10px" });
max_label.prependTo(this.container_div);
// Create canvas
var canvas = this.view.canvas_manager.new_canvas();
canvas.width = width + left_offset;
// Extra padding at top of summary tree
canvas.height = required_height + SUMMARY_TREE_TOP_PADDING;
// Paint summary tree into canvas.
var binned_data = this.get_summary_tree_data(result.data, tile_low, tile_high, 200);
var painter = new painters.SummaryTreePainter(binned_data, tile_low, tile_high, this.prefs);
var ctx = canvas.getContext("2d");
// Deal with left_offset by translating
ctx.translate(left_offset, SUMMARY_TREE_TOP_PADDING);
painter.draw(ctx, width, required_height);
// Canvas element is returned
return canvas;
}
// Start dealing with row-by-row tracks
@@ -3090,43 +3241,6 @@ extend( VariantPainter.prototype, FeaturePainter.prototype, {
}
});
/**
* Compute the type of overlap between two regions. They are assumed to be on the same chrom/contig.
* The overlap is computed relative to the second region; hence, OVERLAP_START indicates that the first
* region overlaps the start (but not the end) of the second region.
*/
var NO_OVERLAP = 1001, CONTAINS = 1002, OVERLAP_START = 1003, OVERLAP_END = 1004, CONTAINED_BY = 1005;
var compute_overlap = function(first_region, second_region) {
var
first_start = first_region[0], first_end = first_region[1],
second_start = second_region[0], second_end = second_region[1],
overlap;
if (first_start < second_start) {
if (first_end < second_start) {
overlap = NO_OVERLAP;
}
else if (first_end <= second_end) {
overlap = OVERLAP_START;
}
else { // first_end > second_end
overlap = CONTAINS;
}
}
else { // first_start >= second_start
if (first_start > second_end) {
overlap = NO_OVERLAP;
}
else if (first_end <= second_end) {
overlap = CONTAINED_BY;
}
else {
overlap = OVERLAP_END;
}
}
return overlap;
}
var ReadPainter = function( data, view_start, view_end, prefs, mode, ref_seq ) {
FeaturePainter.call( this, data, view_start, view_end, prefs, mode );
this.ref_seq = ref_seq;
@@ -3208,8 +3322,7 @@ extend( ReadPainter.prototype, FeaturePainter.prototype, {
case "S": // Soft clipping.
case "M": // Match.
case "=": // Equals.
var seq_tile_overlap = compute_overlap([seq_start, seq_start + cig_len], tile_region);
if (seq_tile_overlap !== NO_OVERLAP) {
if (is_overlap([seq_start, seq_start + cig_len], tile_region)) {
// Draw.
var seq = orig_seq.slice(seq_offset, seq_offset + cig_len);
if (gap > 0) {
@@ -3258,11 +3371,9 @@ extend( ReadPainter.prototype, FeaturePainter.prototype, {
case "I": // Insertion.
// Check to see if sequence should be drawn at all by looking at the overlap between
// the sequence region and the tile region.
var
seq_tile_overlap = compute_overlap([seq_start, seq_start + cig_len], tile_region),
insert_x_coord = s_start - gap;
var insert_x_coord = s_start - gap;
if (seq_tile_overlap !== NO_OVERLAP) {
if (is_overlap([seq_start, seq_start + cig_len], tile_region)) {
var seq = orig_seq.slice(seq_offset, seq_offset + cig_len);
// Insertion point is between the sequence start and the previous base: (-gap) moves
// back from sequence start to insertion point.