1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/116d7867f3f8/ Changeset: 116d7867f3f8 User: guerler Date: 2014-05-03 21:39:40 Summary: Charts: Implement heatmap sort for sparse data Affected #: 1 file
diff -r fd8cf23297536147d5bbeed5b8b5d501eb8e84bf -r 116d7867f3f8efca5fdc2998bb3bb5df55724529 config/plugins/visualizations/charts/static/charts/heatmap/heatmap-plugin.js --- a/config/plugins/visualizations/charts/static/charts/heatmap/heatmap-plugin.js +++ b/config/plugins/visualizations/charts/static/charts/heatmap/heatmap-plugin.js @@ -20,19 +20,24 @@ // cell size cellSize: 0,
+ // font size + fontSize: 0, + // color buckets nColors: 0, - + + // margins as cells + margin : { + top : 5, + right : 5, + bottom : 5, + left : 5 + }, + // default settings optionsDefault: { title : '', pace : 1000, - margin : { - top : 50, - right : 10, - bottom : 50, - left : 100 - } },
// initialize @@ -107,20 +112,19 @@ // generate sorted key list for rows for (var i in this.rowLabel) { var row_label = this.rowLabel[i]; - var row_rank = parseInt(i); - this.rowRank[row_label] = row_rank; + var row = parseInt(i); + this.rowRank[row_label] = row; }
// generate sorted key list for columns for (var i in this.colLabel) { var col_label = this.colLabel[i]; - var col_rank = parseInt(i); - this.colRank[col_label] = col_rank; + var col = parseInt(i); + this.colRank[col_label] = col; }
// // parse indexing from rank dictionary to cells - // identify data range //
// min/max @@ -133,8 +137,8 @@ var cell = this.data[i];
// add rank - cell.col_rank = this.colRank[cell.col_label]; - cell.row_rank = this.rowRank[cell.row_label]; + cell.col = this.colRank[cell.col_label]; + cell.row = this.rowRank[cell.row_label];
// identify max/min values if (this.min == undefined || this.min > cell.value) { @@ -199,17 +203,20 @@ // link this var self = this;
- // container - var container_width = this.$el.width(); - var container_height = this.$el.height(); + // container (full draw area) + this.widthContainer = this.$el.width(); + this.heightContainer = this.$el.height();
- // get height - this.width = this.$el.width() - this.options.margin.left - this.options.margin.right; - this.height = this.$el.height() - this.options.margin.top - this.options.margin.bottom; + // get grid dimensions + this.width = this.widthContainer; + this.height = this.heightContainer;
// calculate cell size - this.cellSize = Math.min(parseInt(this.height / this.rowNumber), - parseInt(this.width / this.colNumber)); + this.cellSize = Math.min(((this.height - 50) / (this.rowNumber + this.margin.top + this.margin.bottom)), + (this.width / (this.colNumber + this.margin.left + this.margin.right))); + + // set font size + this.fontSize = Math.min(this.cellSize, 16);
// set width/height for plugin this.width = this.cellSize * this.colNumber; @@ -222,10 +229,9 @@
// add main group and translate this.svg = d3.select(this.$el[0]).append('svg') - .attr('width', width + margin.left + margin.right) - .attr('height', height + margin.top + margin.bottom) .append('g') - .attr('transform', 'translate(' + (container_width - width) / 2 + ',' + (container_height - height) / 2 + ')') + .attr('transform', 'translate(' + (this.widthContainer - width) / 2 + ',' + + (this.heightContainer - height) / 2 + ')')
// reset sorting this.rowSortOrder = false; @@ -245,15 +251,17 @@ var self = this;
// gather data - var height = this.height; - var width = this.width; - var title = this.options.title; + var height = this.height; + var width = this.width; + var cellSize = this.cellSize; + var fontSize = this.fontSize; + var title = this.options.title;
// add title this.svg.append('g') .append('text') .attr('x', width / 2) - .attr('y', height - 10) + .attr('y', height + 3 * cellSize + fontSize + 3) .attr('text-anchor', 'middle') .text(title); }, @@ -265,6 +273,7 @@
// gather data var cellSize = this.cellSize; + var fontSize = this.fontSize; var height = this.height; var legendCellWidth = this.width / this.nColors;
@@ -312,8 +321,8 @@ .attr('x', function(d, i) { return legendCellWidth * i; }) - .attr('y', height + cellSize) - .style('font-size', cellSize + 'px'); + .attr('y', height + cellSize - 3) + .style('font-size', fontSize + 'px'); },
// build column labels @@ -323,6 +332,7 @@
// gather data var cellSize = this.cellSize; + var fontSize = this.fontSize; var colIndex = this.colIndex; var colLabel = this.colLabel;
@@ -339,7 +349,7 @@ .attr('y', function (d, i) { return colIndex.indexOf(i) * cellSize; }) - .style('font-size', cellSize + 'px') + .style('font-size', fontSize + 'px') .style('text-anchor', 'left') .attr('transform', 'translate(' + cellSize / 2 + ', -17) rotate (-90)') .attr('class', function (d, i) { @@ -347,15 +357,13 @@ }) .on('mouseover', function(d) { d3.select(this).classed('text-hover',true); - d3.select(this).style('font-size', parseInt(cellSize * 1.3) + 'px'); }) .on('mouseout' , function(d) { d3.select(this).classed('text-hover',false); - d3.select(this).style('font-size', parseInt(cellSize) + 'px'); }) .on('click', function(d, i) { self.colSortOrder=!self.colSortOrder; - self._sortByLabel('c', i, self.colSortOrder); + self._sortByLabel('c', 'row', self.rowNumber, i, self.colSortOrder); d3.select('#order').property('selectedIndex', 4).node().focus(); }); }, @@ -367,6 +375,7 @@
// gather data var cellSize = this.cellSize; + var fontSize = this.fontSize; var rowIndex = this.rowIndex; var rowLabel = this.rowLabel;
@@ -383,7 +392,7 @@ .attr('y', function (d, i) { return rowIndex.indexOf(i) * cellSize; }) - .style('font-size', cellSize + 'px') + .style('font-size', fontSize + 'px') .style('text-anchor', 'end') .attr('transform', 'translate(-10,' + cellSize / 1.5 + ')') .attr('class', function (d, i) { @@ -391,15 +400,13 @@ } ) .on('mouseover', function(d) { d3.select(this).classed('text-hover',true); - d3.select(this).style('font-size', parseInt(cellSize * 1.3) + 'px'); }) .on('mouseout' , function(d) { d3.select(this).classed('text-hover',false); - d3.select(this).style('font-size', parseInt(cellSize) + 'px'); }) .on('click', function(d, i) { self.rowSortOrder=!self.rowSortOrder; - self._sortByLabel('r', i, self.rowSortOrder); + self._sortByLabel('r', 'col', self.colNumber, i, self.rowSortOrder); d3.select('#order').property('selectedIndex', 4).node().focus(); }); }, @@ -420,18 +427,18 @@ var heatMap = this.svg.append('g').attr('class','g3') .selectAll('.cellg') .data(self.data, function(d) { - return d.row_rank + ':' + d.col_rank; + return d.row + ':' + d.col; }) .enter() .append('rect') .attr('x', function(d) { - return colIndex.indexOf(d.col_rank) * cellSize; + return colIndex.indexOf(d.col) * cellSize; }) .attr('y', function(d) { - return rowIndex.indexOf(d.row_rank) * cellSize; + return rowIndex.indexOf(d.row) * cellSize; }) .attr('class', function(d){ - return 'cell cell-border cr' + d.row_rank + ' cc' + d.col_rank; + return 'cell cell-border cr' + d.row + ' cc' + d.col; }) .attr('width', cellSize) .attr('height', cellSize) @@ -441,15 +448,15 @@ .on('mouseover', function(d){ // highlight text d3.select(this).classed('cell-hover',true); - d3.selectAll('.rowLabel').classed('text-highlight',function(r,ri){ return ri==(d.row_rank);}); - d3.selectAll('.colLabel').classed('text-highlight',function(c,ci){ return ci==(d.col_rank);}); + d3.selectAll('.rowLabel').classed('text-highlight',function(r,ri){ return ri==(d.row);}); + d3.selectAll('.colLabel').classed('text-highlight',function(c,ci){ return ci==(d.col);});
// update the tooltip position and value d3.select('#heatmap-tooltip') .style('left', (d3.event.pageX+10) + 'px') .style('top', (d3.event.pageY-10) + 'px') .select('#value') - .text('Label: ' + rowLabel[d.row_rank] + ' | ' + colLabel[d.col_rank] + ', Value: ' + d.value); + .text('Label: ' + rowLabel[d.row] + ' | ' + colLabel[d.col] + ', Value: ' + d.value); // show the tooltip d3.select('#heatmap-tooltip').classed('hidden', false); }) @@ -462,18 +469,25 @@ },
// change ordering of cells - _sortByLabel: function(rORc, i, sortOrder) { + _sortByLabel: function(rORc, rowORcol, n, index, sortOrder) { // get cell size var cellSize = this.cellSize;
// define transition / prepare element var t = this.svg.transition().duration(this.options.pace);
+ // create cells + var cells=[]; + for (var i = 0; i < n; i++) { + cells[i] = { + value: this.min - 1 + } + cells[i][rowORcol] = i; + } + // collect cells - var cells=[]; - t.selectAll('.c' + rORc + i) - .filter(function(ce){ - cells.push(ce); + t.selectAll('.c' + rORc + index).filter(function(ce) { + cells[ce[rowORcol]].value = ce.value; });
// sort cells @@ -484,19 +498,19 @@ return a.value - b.value; } }); - + + // get sorted key list + var sorted = []; + for (var i in cells) { + sorted.push(cells[i][rowORcol]); + } + // rows or columns if(rORc == 'r') { - // get sorted key list - var sorted = []; - for (var i in cells) { - sorted.push(cells[i].col_rank); - } - // sort cells t.selectAll('.cell') .attr('x', function(d) { - return sorted.indexOf(d.col_rank) * cellSize; + return sorted.indexOf(d.col) * cellSize; });
// sort labels @@ -505,23 +519,17 @@ return sorted.indexOf(i) * cellSize; }); } else { - // get sorted key list - sorted = []; - for (var i in cells) { - sorted.push(cells[i].row_rank); - } - // sort cells t.selectAll('.cell') .attr('y', function(d) { - return sorted.indexOf(d.row_rank) * cellSize; - }); - + return sorted.indexOf(d.row) * cellSize; + }); + // sort labels t.selectAll('.rowLabel') .attr('y', function (d, i) { return sorted.indexOf(i) * cellSize; - }); + }); } },
@@ -542,10 +550,10 @@ if(value=='hclust'){ t.selectAll('.cell') .attr('x', function(d) { - return colIndex.indexOf(d.col_rank) * cellSize; + return colIndex.indexOf(d.col) * cellSize; }) .attr('y', function(d) { - return rowIndex.indexOf(d.row_rank) * cellSize; + return rowIndex.indexOf(d.row) * cellSize; });
t.selectAll('.rowLabel') @@ -561,10 +569,10 @@ } else if (value=='byboth') { t.selectAll('.cell') .attr('x', function(d) { - return d.col_rank * cellSize; + return d.col * cellSize; }) .attr('y', function(d) { - return d.row_rank * cellSize; + return d.row * cellSize; });
t.selectAll('.rowLabel') @@ -579,7 +587,7 @@ } else if (value=='byrow') { t.selectAll('.cell') .attr('y', function(d) { - return d.row_rank * cellSize; + return d.row * cellSize; });
t.selectAll('.rowLabel') @@ -589,7 +597,7 @@ } else if (value=='bycol'){ t.selectAll('.cell') .attr('x', function(d) { - return d.col_rank * cellSize; + return d.col * cellSize; }); t.selectAll('.colLabel') .attr('y', function (d, i) { @@ -666,11 +674,11 @@ .classed('cell-selection', true) .classed('cell-selected', true);
- d3.select('.r'+(cell_d.row_rank)) + d3.select('.r' + cell_d.row) .classed('text-selection',true) .classed('text-selected',true);
- d3.select('.c'+(cell_d.col_rank)) + d3.select('.c' + cell_d.col) .classed('text-selection',true) .classed('text-selected',true); }
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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