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Gosling GFF viz
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‎src/components/Result/GoslingViz.js

Lines changed: 81 additions & 89 deletions
Original file line numberDiff line numberDiff line change
@@ -33,6 +33,7 @@ function GoslingGenomeViz({ dataKey, showPlot, filter }) {
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}
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const spec = {
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"arrangement": "vertical",
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"spacing": 50,
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"views": getViews(data["data"])
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};
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console.log(spec);
@@ -47,68 +48,102 @@ function GoslingGenomeViz({ dataKey, showPlot, filter }) {
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const createGeneTrack = (data) => {
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const GeneTrackcreator = (data, strand) => {
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return {
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"data": {
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"values": data,
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"type": "json",
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"genomicFields": ["start", "end"]
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},
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return [{
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"alignment": "overlay",
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"data": {
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"values": data,
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"type": "json",
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"genomicFields": ["start", "end"]
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},
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"row": { "field": "strand", "type": "nominal", "domain": ["+", "-"] },
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"mark": "rect",
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"x": { "field": "start", "type": "genomic", "axis": "none" },
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"xe": { "field": "end", "type": "genomic", "axis": "none" },
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"color": { "value": "grey" },
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"opacity": { "value": 0.4 },
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"size": { "value": 4 },
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"tracks": [{
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"dataTransform": [
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{ "type": "filter", "field": "strand", "oneOf": "+" }
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],
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}, {
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"dataTransform": [
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{ "type": "filter", "field": "strand", "oneOf": [strand] }
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{ "type": "filter", "field": "strand", "oneOf": "-" }
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],
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"mark": "rect",
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"row": { "field": "strand", "type": "nominal", "domain": ["+", "-"] },
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"x": { "field": "start", "type": "genomic", "axis": "top" },
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"xe": { "field": "end", "type": "genomic", "axis": "top" },
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"color": { "value": "grey" },
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"style": { "opacity": 0.2 },
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"size": { "value": 5 }
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}
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}
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]
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}]
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return [GeneTrackcreator(data, "+"), GeneTrackcreator(data, "-")]
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}
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74-
const createTSSTrack = (data) => {
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const TSSTrackcreator = (data, strand) => {
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return {
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const createTSSTrack = (data, strand, title = null) => {
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return [
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{
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"title": title,
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"alignment": "overlay",
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"data": {
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"values": data.filter(d => filter.includes(d["typeTSS"])),
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"type": "json",
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"genomicFields": ["superPos"]
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"genomicFields": ["superPos"],
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},
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"row": { "field": "superStrand", "type": "nominal", "domain": ["+", "-"] },
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"dataTransform": [
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{ "type": "filter", "field": "superStrand", "oneOf": strand }
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],
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"mark": strand === "+" ? "triangleRight" : "triangleLeft",
87-
"x": { "field": "superPos", "type": "genomic", "axis": "top" },
93+
// "row": { "field": "superStrand", "type": "nominal", "domain": ["+", "-"] },
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// "mark": "point",
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// "x": { "field": "superPos", "type": "genomic", "axis": "top" },
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"color": {
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"field": "mainClass",
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"type": "nominal",
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"domain": ["Primary", "Secondary", "Internal", "Antisense", "Orphan"],
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"range": ["#7585FF", "#FF8A85", "#FFC785", "#85FFD9", "#B285FF"],
94-
"legend": true
103+
"legend": strand === "+"
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},
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"tracks": [{
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"dataTransform": [
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{ "type": "filter", "field": "superStrand", "oneOf": [strand] }
108+
],
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"x": { "field": "superPos", "type": "genomic", "axis": strand === "+" ? "top" : "none" },
110+
"mark": strand === "+" ? "triangleRight" : "triangleLeft",
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"style": { "align": strand === "+" ? "left" : "right" },
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"size": { "value": 15 },
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},
96-
"style": { "align": strand === "+" ? "right" : "left" },
97-
"size": { "value": 15 }
114+
{
115+
"data": {
116+
"values": data.filter(d => filter.includes(d["typeTSS"])),
117+
"type": "json",
118+
"genomicFields": ["superPos"],
119+
"binSize": 10,
120+
},
121+
"dataTransform": [
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{ "type": "filter", "field": "superStrand", "oneOf": [strand] }
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],
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"x": { "field": "superPos", "type": "genomic", "aggregate": "bin", "axis": "none" },
125+
"xe": { "field": "superPos", "type": "genomic" },
126+
// "size": { "value": 10 },
127+
"y": {
128+
"field": "mainClass", "type": "nominal", "axis": "none",
129+
"domain": ["Primary", "Secondary", "Internal", "Antisense", "Orphan"],
130+
"range": [50, 50, 50, 50, 50],
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"aggregate": "count"
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133+
},
134+
"mark": "bar",
135+
// "y": { "type": "quantitative", "axis": "none" },
136+
}]
98137
}
99-
}
100-
101-
return [
102-
TSSTrackcreator(data, "-"),
103-
TSSTrackcreator(data, "+")
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105139
]
106140
}
107141

108-
const createTracks = (data) => {
142+
const createTracks = (data, title) => {
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let geneTracks = createGeneTrack(data["superGFF"]);
110-
let TSSTracks = createTSSTrack(data["TSS"]);
111-
return geneTracks.concat(TSSTracks);
144+
let TSSTracks_plus = createTSSTrack(data["TSS"], "+", title);
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let TSSTracks_minus = createTSSTrack(data["TSS"], "-");
146+
return TSSTracks_plus.concat(geneTracks).concat(TSSTracks_minus);
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}
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@@ -117,67 +152,24 @@ function GoslingGenomeViz({ dataKey, showPlot, filter }) {
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console.log(data);
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for (let genome of Object.keys(data)) {
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views.push({
120-
"alignment": "overlay",
155+
"alignment": "stack",
121156
"title": genome,
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"assembly": [["", data[genome]["maxValue"]]],
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124-
"tracks": createTracks(data[genome])
158+
"spacing": 0,
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"layout": "linear",
160+
"tracks": createTracks(data[genome], genome,)
125161
})
126162
}
127163
return views;
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129165
}
130166

131-
return <div className={showPlot ? '' : 'hidden'}>
132-
{spec && <GoslingComponent spec={spec} />}
133-
</div>;
167+
return spec && <GoslingComponent spec={spec} />
168+
169+
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135171
}
136172

137-
// "alignment": "overlay",
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// "title": "Position of TSSs",
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// "assembly": [["", 250000]],
140-
// "data": {
141-
// "values": data,
142-
// "type": "json",
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// "genomicFields": ["pos"]
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// },
145-
// "row": { "field": "strand", "type": "nominal", "domain": ["+", "-"] },
146-
// "color": {
147-
// "field": "mainClass",
148-
// "type": "nominal",
149-
// "domain": ["primary", "secondary", "internal", "antisense", "orphan"],
150-
// "range": ["#7585FF", "#FF8A85", "#FFC785", "#85FFD9", "#B285FF"],
151-
// "legend": true
152-
// },
153-
// "visibility": [
154-
// {
155-
// "operation": "less-than",
156-
// "measure": "width",
157-
// "threshold": "|xe-x|",
158-
// "transitionPadding": 10,
159-
// "target": "mark"
160-
// }
161-
// ],
162-
// "opacity": { "value": 0.8 },
163-
// "width": 350,
164-
// "height": 100,
165-
// "tracks": [
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// ,
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// {
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// "dataTransform": [
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// { "type": "filter", "field": "strand", "oneOf": ["-"] }
170-
// ],
171-
// "mark": "triangleLeft",
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// "x": { "field": "pos", "type": "genomic" },
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// "size": { "value": 15 },
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// "style": { "align": "right" }
175-
176-
// }
177-
// ]
178-
// }
179-
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181-
// }
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export default GoslingGenomeViz

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