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Trackster: improve display of allele summaries.

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This commit is contained in:
Jeremy Goecks
2014-10-24 16:29:53 -04:00
parent bda44d0daf
commit e7d1acd6d3
3 changed files with 35 additions and 33 deletions
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client/galaxy/scripts/viz/trackster/painters.js
+17 -16
View File
@@ -1519,7 +1519,7 @@ _.extend(VariantPainter.prototype, Painter.prototype, {
alt = [ locus_data[4].split(',') ];
sample_gts = locus_data[7].split(',');
allele_counts = locus_data.slice(8);
// Process alterate values to derive information about each alt.
alt = _.map(_.flatten(alt), function(a) {
var alt_info = {
@@ -1537,23 +1537,23 @@ _.extend(VariantPainter.prototype, Painter.prototype, {
continue;
}
// Compute start for drawing variants marker, text.
draw_x_start = this.get_start_draw_pos(pos, w_scale);
// Draw summary.
// Draw summary for alleles.
if (draw_summary) {
ctx.fillStyle = '#999999';
ctx.globalAlpha = 1;
// Draw background for summary.
ctx.fillRect(draw_x_start, 0, base_px, this.prefs.summary_height);
draw_y_start = this.prefs.summary_height;
// Draw allele fractions onto summary.
for (j = 0; j < alt.length; j++) {
ctx.fillStyle = ( alt[j].type === 'deletion' ? 'black' : this.base_color_fn(alt[j].value) );
allele_frac = allele_counts / sample_gts.length;
draw_height = Math.ceil(this.prefs.summary_height * allele_frac);
ctx.fillRect(draw_x_start, draw_y_start - draw_height, base_px, draw_height);
draw_y_start -= draw_height;
for (j = 0; j < alt.length; j++) {
// Draw background for summary.
draw_x_start = this.get_start_draw_pos(pos + alt[j].start, w_scale);
ctx.fillRect(draw_x_start, 0, base_px, this.prefs.summary_height);
draw_y_start = this.prefs.summary_height;
// Draw allele fractions onto summary.
for (j = 0; j < alt.length; j++) {
ctx.fillStyle = ( alt[j].type === 'deletion' ? 'black' : this.base_color_fn(alt[j].value) );
allele_frac = allele_counts / sample_gts.length;
draw_height = Math.ceil(this.prefs.summary_height * allele_frac);
ctx.fillRect(draw_x_start, draw_y_start - draw_height, base_px, draw_height);
draw_y_start -= draw_height;
}
}
}
@@ -1586,6 +1586,7 @@ _.extend(VariantPainter.prototype, Painter.prototype, {
// If there's a variant, draw it.
if (variant) {
draw_x_start = this.get_start_draw_pos(pos + variant.start, w_scale);
if (variant.type === 'snp') {
var snp = variant.value;
ctx.fillStyle = this.base_color_fn(snp);
@@ -1597,7 +1598,7 @@ _.extend(VariantPainter.prototype, Painter.prototype, {
}
}
else if (variant.type === 'deletion') {
paint_utils.draw_deletion(draw_x_start + base_px * variant.start, draw_y_start + 1, variant.len);
paint_utils.draw_deletion(draw_x_start, draw_y_start + 1, variant.len);
}
else {
// TODO: handle insertions.
static/scripts/packed/viz/trackster/painters.js
+1 -1
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static/scripts/viz/trackster/painters.js
+17 -16
View File
@@ -1519,7 +1519,7 @@ _.extend(VariantPainter.prototype, Painter.prototype, {
alt = [ locus_data[4].split(',') ];
sample_gts = locus_data[7].split(',');
allele_counts = locus_data.slice(8);
// Process alterate values to derive information about each alt.
alt = _.map(_.flatten(alt), function(a) {
var alt_info = {
@@ -1537,23 +1537,23 @@ _.extend(VariantPainter.prototype, Painter.prototype, {
continue;
}
// Compute start for drawing variants marker, text.
draw_x_start = this.get_start_draw_pos(pos, w_scale);
// Draw summary.
// Draw summary for alleles.
if (draw_summary) {
ctx.fillStyle = '#999999';
ctx.globalAlpha = 1;
// Draw background for summary.
ctx.fillRect(draw_x_start, 0, base_px, this.prefs.summary_height);
draw_y_start = this.prefs.summary_height;
// Draw allele fractions onto summary.
for (j = 0; j < alt.length; j++) {
ctx.fillStyle = ( alt[j].type === 'deletion' ? 'black' : this.base_color_fn(alt[j].value) );
allele_frac = allele_counts / sample_gts.length;
draw_height = Math.ceil(this.prefs.summary_height * allele_frac);
ctx.fillRect(draw_x_start, draw_y_start - draw_height, base_px, draw_height);
draw_y_start -= draw_height;
for (j = 0; j < alt.length; j++) {
// Draw background for summary.
draw_x_start = this.get_start_draw_pos(pos + alt[j].start, w_scale);
ctx.fillRect(draw_x_start, 0, base_px, this.prefs.summary_height);
draw_y_start = this.prefs.summary_height;
// Draw allele fractions onto summary.
for (j = 0; j < alt.length; j++) {
ctx.fillStyle = ( alt[j].type === 'deletion' ? 'black' : this.base_color_fn(alt[j].value) );
allele_frac = allele_counts / sample_gts.length;
draw_height = Math.ceil(this.prefs.summary_height * allele_frac);
ctx.fillRect(draw_x_start, draw_y_start - draw_height, base_px, draw_height);
draw_y_start -= draw_height;
}
}
}
@@ -1586,6 +1586,7 @@ _.extend(VariantPainter.prototype, Painter.prototype, {
// If there's a variant, draw it.
if (variant) {
draw_x_start = this.get_start_draw_pos(pos + variant.start, w_scale);
if (variant.type === 'snp') {
var snp = variant.value;
ctx.fillStyle = this.base_color_fn(snp);
@@ -1597,7 +1598,7 @@ _.extend(VariantPainter.prototype, Painter.prototype, {
}
}
else if (variant.type === 'deletion') {
paint_utils.draw_deletion(draw_x_start + base_px * variant.start, draw_y_start + 1, variant.len);
paint_utils.draw_deletion(draw_x_start, draw_y_start + 1, variant.len);
}
else {
// TODO: handle insertions.