Merge pull request #225 from broadinstitute/integration

Integration

locusBrowser/README.md

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+### LocusBrowser
+
+To run the demo of LocusBrowser locally:
+Start a light-weight http server in this directory
+```python3 -m http.server```
+
+And launch the URL (http://0.0.0.0:8000/) from a browser.

locusBrowser/css/boxplot.css

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+div.boxplot-tooltip {
+   min-width: 100px;
+   display: none;
+   background-color : rgba(32, 53, 73, 0.95);
+   padding: 10px;
+   text-align:left;
+   color: #ffffff;
+   position:absolute;
+   font-size:12px;
+   z-index:4000;
+   border-radius:5px;
+}

locusBrowser/css/bubbleMap.css

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+/**
+ * Copyright © 2015 - 2018 The Broad Institute, Inc. All rights reserved.
+ * Licensed under the BSD 3-clause license (https://github.com/broadinstitute/gtex-viz/blob/master/LICENSE.md)
+ */
+text.color-legend {
+    font-family: "Open Sans", "Helvetica", "Arial", sans-serif;
+    font-size: 10px;
+}
+
+text.bubble-map-xlabel {
+    font-family: "Open Sans", "Helvetica", "Arial", sans-serif;
+    /*font-size: 10px;*/
+}
+text.bubble-map-xlabel.highlighted {
+    font-weight: 400;
+    /*font-size: 12px;*/
+    text-decoration: underline;
+}
+text.bubble-map-xlabel.query {
+    font-weight: 600;
+    /*font-size:11px;*/
+    fill: #d2111b;
+}
+
+text.bubble-map-ylabel {
+    font-family: "Open Sans", "Helvetica", "Arial", sans-serif;
+    /*font-size: 10px;*/
+}
+text.bubble-map-ylabel.highlighted {
+    font-weight: 400;
+    /*font-size: 12px;*/
+    text-decoration: underline;
+}
+text.bubble-map-ylabel.clicked, text.bubble-map-xlabel.clicked {
+    fill: #D25C43;
+}
+
+circle.bubble-map-cell {
+    stroke-width:0px;
+}
+circle.bubble-map-cell.highlighted {
+    stroke: #D25C43;
+    stroke-width:2px;
+}
+
+rect.mini-marker {
+    fill: none;
+}
+
+rect.mini-marker.highlighted {
+    fill: #D25C43;
+}
+
+div.bubblemap-tooltip {
+   min-width: 100px;
+   display: none;
+   background-color : rgba(32, 53, 73, 0.95);
+   padding: 10px;
+   text-align:left;
+   color: #ffffff;
+   position:absolute;
+   font-size:12px;
+   z-index:4000;
+   border-radius:5px;
+}
+
+rect.track.highlighted {
+    stroke: #D25C43;
+}
+
+/* eQTL box plot stuff */
+.closePlot {
+   cursor:pointer;
+   float:right;
+}
+
+.bbMap-canvas {
+    margin-top: 30px;
+    margin-left: 250px;
+}
+
+.bbMap-dialog .title {
+   text-align: center;
+   font-size: 12px;
+
+}
+
+/*#bbMap-dialog text.plotviz-label {*/
+   /*font-size: 12px;*/
+/*}*/
+
+/*#bbMap-dialog .plotviz-left-axis g.tick text {*/
+   /*font-size: 11px;*/
+/*}*/
+
+#bbMap-dialog {
+   font-size: 11px;
+}
+
+.violin-axis-label {
+    font-size: 10px;
+}
+
+.bbMap-clear {
+   color: #999;
+   font-size: 10px;
+   text-decoration: underline;
+   cursor: pointer;
+}
+
+/* jquery UI customization */
+.ui-dialog .ui-dialog-titlebar {
+   padding: 0.1em 0.2em;
+}
+
+.ui-dialog-content {
+   width: 100% !important; /* this is an important overwrite that ensures that the ui-dialog-content's width remains 100% of the ui-dialog after a resizing event */
+}
+
+.ui-widget-header {
+   border: 0px;
+}
+.ui-dialog {
+    z-index:2000;
+}
+
+
+

locusBrowser/css/dendrogram.css

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+/**
+ * Copyright © 2015 - 2018 The Broad Institute, Inc. All rights reserved.
+ * Licensed under the BSD 3-clause license (https://github.com/broadinstitute/gtex-viz/blob/master/LICENSE.md)
+ */
+.dendrogram-axis line, .dendrogram-axis path{
+  fill: none;
+  stroke: #a9a9a9;
+  shape-rendering: crispEdges;
+}
+
+.dendrogram-axis text {
+    fill: #a9a9a9;
+}
+
+.leaf-color {
+    stroke-width: 0;
+}
+
+.leaf-color.highlighted {
+    stroke-width: 1px;
+    stroke: #555f66;
+}

locusBrowser/css/eqtlDashboard.css

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+/**
+ * Copyright © 2015 - 2018 The Broad Institute, Inc. All rights reserved.
+ * Licensed under the BSD 3-clause license (https://github.com/broadinstitute/gtex-viz/blob/master/LICENSE.md)
+ */
+.ed-section-title {
+    font-family: "Open Sans", "Helvetica", "Arial", sans-serif;
+    font-size: 15px;
+}

locusBrowser/css/expressMap.css

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+/**
+ * Copyright © 2015 - 2018 The Broad Institute, Inc. All rights reserved.
+ * Licensed under the BSD 3-clause license (https://github.com/broadinstitute/gtex-viz/blob/master/LICENSE.md)
+ */
+text.color-legend {
+    font-family: "Open Sans", "Helvetica", "Arial", sans-serif;
+    font-size: 10px;
+}
+
+text.exp-map-xlabel {
+    font-family: "Open Sans", "Helvetica", "Arial", sans-serif;
+    font-size: 10px;
+}
+text.exp-map-xlabel.highlighted {
+    font-weight: 400;
+    font-size: 12px;
+    text-decoration: underline;
+}
+text.exp-map-xlabel.query {
+    font-weight: 600;
+    font-size:11px;
+    fill: #d2111b;
+}
+
+
+text.exp-map-ylabel {
+    font-family: "Open Sans", "Helvetica", "Arial", sans-serif;
+    font-size: 10px;
+}
+text.exp-map-ylabel.highlighted {
+    font-weight: 400;
+    font-size: 12px;
+    text-decoration: underline;
+}
+text.exp-map-ylabel.clicked, text.exp-map-xlabel.clicked {
+    fill: #D25C43;
+}
+
+rect.exp-map-cell {
+    stroke-width:0px;
+}
+rect.exp-map-cell.highlighted {
+    stroke: #D25C43;
+    stroke-width:2px;
+}
+
+div.heatmap-tooltip {
+   min-width: 100px;
+   display: none;
+   background-color : rgba(32, 53, 73, 0.95);
+   padding: 10px;
+   text-align:left;
+   color: #ffffff;
+   position:absolute;
+   font-size:12px;
+   z-index:4000;
+   border-radius:5px;
+}
+
+
+

locusBrowser/css/geneExpViolin.css

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+#gene-expr-vplot-toolbar-plot-options {
+    display: inline-flex;
+}
+
+#gene-expr-vplot-toolbar-plot-options label {
+    margin-bottom: 0;
+}
+
+#gene-expr-vplot-toolbar {
+    border-bottom: 1px solid #e2e2e2;
+    border-top: 1px solid #e2e2e2;
+    padding: 5px 0px 5px 0px;
+}
+
+.gene-expr-vplot-option-label {
+    padding-right: 5px;
+    font-size: 15px;
+    font-variant: all-small-caps;
+    font-weight: 500;
+}
+
+#gene-expr-vplot-svg .violin-x-axis line, #gene-expr-vplot-svg .violin-y-axis line, #gene-expr-vplot-svg  .violin-x-axis path, #gene-expr-vplot-svg  .violin-y-axis path{
+    stroke: Black;
+}
+
+#gene-expr-vplot-svg .violin-x-axis text, #gene-expr-vplot-svg  .violin-y-axis text, #gene-expr-vplot-svg  .violin-axis-label {
+    fill: Black;
+    font-size: 11.5px;
+    font-weight: 500;
+}
+
+#gene-expr-vplot-svg text.violin-axis-label {
+    font-size: 12px;
+}
+
+#gene-expr-vplot-svg text.violin-legend-text {
+    font-size: 11.5px;
+    fill: Black;
+    font-weight: 500;
+}
+
+#gene-expr-vplot-svg path.violin.outlined {
+    stroke-width: 1.2px;
+    stroke: rgba(170, 170, 170, 0.9);
+}
+
+#gene-expr-vplot-svg path.violin.highlighted {
+    stroke-width: 2px;
+    stroke: rgba(85, 95, 102, 1);
+}
+
+#gene-expr-vplot-svg path.violin.highlighted.outlined {
+    stroke-width: 2px;
+    stroke: rgba(85, 95, 102, 1);
+}

locusBrowser/css/gtex-private.code-workspace

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+{
+	"folders": [
+		{
+			"path": "/Users/khhuang/Sites/gtex-viz-private"
+		}
+	]
+}

locusBrowser/css/halfMap.css

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+/**
+ * Copyright © 2015 - 2018 The Broad Institute, Inc. All rights reserved.
+ * Licensed under the BSD 3-clause license (https://github.com/broadinstitute/gtex-viz/blob/master/LICENSE.md)
+ */
+text.color-legend {
+    font-family: "Open Sans", "Helvetica", "Arial", sans-serif;
+    font-size: 10px;
+}
+
+text.half-map-label {
+    font-family: "Open Sans", "Helvetica", "Arial", sans-serif;
+    font-size: 10px;
+}
+text.half-map-label.highlighted {
+    font-weight: 400;
+    font-size: 12px;
+    text-decoration: underline;
+}
+
+div.half-map-tooltip {
+   min-width: 100px;
+   display: none;
+   background-color : rgba(32, 53, 73, 0.95);
+   padding: 10px;
+   text-align:left;
+   color: #ffffff;
+   position:absolute;
+   font-size:12px;
+   z-index:4000;
+   border-radius:5px;
+}
+
+
+