Created
March 29, 2021 22:57
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GOSLING: Comparison of Micro-C and Hi-C for HFFc6 Cells
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{ | |
"title": "Matrix Visualization", | |
"subtitle": "Comparison of Micro-C and Hi-C for HFFc6 Cells", | |
"arrangement": "horizontal", | |
"xDomain": {"chromosome": "7", "interval": [77700000, 81000000]}, | |
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"type": "vector", | |
"column": "position", | |
"value": "peak" | |
}, | |
"title": "HFFc6_H3K4me3", | |
"mark": "bar", | |
"x": {"field": "position", "type": "genomic", "axis": "none"}, | |
"y": {"field": "peak", "type": "quantitative"}, | |
"color": {"value": "darkgreen"}, | |
"style": {"outline": "gray"}, | |
"width": 570, | |
"height": 40 | |
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{ | |
"data": { | |
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"type": "vector", | |
"column": "position", | |
"value": "peak" | |
}, | |
"title": "HFFc6_ATAC", | |
"mark": "bar", | |
"x": {"field": "position", "type": "genomic"}, | |
"y": {"field": "peak", "type": "quantitative"}, | |
"color": {"value": "purple"}, | |
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"type": "vector", | |
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"mark": "bar", | |
"x": {"field": "position", "type": "genomic"}, | |
"y": {"field": "peak", "type": "quantitative"}, | |
"color": {"value": "blue"} | |
}, | |
{ | |
"data": { | |
"url": "https://higlass.io/api/v1/tileset_info/?d=EkPGY0iFQx6Nq6vdF8CpWA", | |
"type": "beddb", | |
"genomicFields": [ | |
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{"index": 2, "name": "end"} | |
], | |
"valueFields": [ | |
{"index": 5, "name": "strand", "type": "nominal"}, | |
{"index": 3, "name": "name", "type": "nominal"} | |
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"x": {"field": "start", "type": "genomic"}, | |
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"row": { | |
"field": "strand", | |
"type": "nominal", | |
"domain": ["+", "-"] | |
}, | |
"color": {"value": "red"} | |
}, | |
{ | |
"title": "HFFC6_CTCF", | |
"data": { | |
"url": "https://higlass.io/api/v1/tileset_info/?d=EkPGY0iFQx6Nq6vdF8CpWA", | |
"type": "beddb", | |
"genomicFields": [ | |
{"index": 1, "name": "start"}, | |
{"index": 2, "name": "end"} | |
], | |
"valueFields": [ | |
{"index": 5, "name": "strand", "type": "nominal"}, | |
{"index": 3, "name": "name", "type": "nominal"} | |
] | |
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"dataTransform": { | |
"filter": [{"field": "strand", "oneOf": ["-"]}] | |
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"mark": "triangleLeft", | |
"x": {"field": "start", "type": "genomic"}, | |
"stroke": {"value": "white"}, | |
"strokeWidth": {"value": 1}, | |
"size": {"value": 10}, | |
"row": { | |
"field": "strand", | |
"type": "nominal", | |
"domain": ["+", "-"] | |
}, | |
"color": {"value": "green"} | |
} | |
], | |
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} | |
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}, | |
{ | |
"tracks": [ | |
{ | |
"title": "HFFc6_Micro-C", | |
"data": { | |
"url": "https://resgen.io/api/v1/tileset_info/?d=bRCUQ7NhQS-6LU61SxAQ0Q", | |
"type": "matrix" | |
}, | |
"mark": "rect", | |
"x": {"field": "position1", "type": "genomic", "axis": "top"}, | |
"y": {"field": "position2", "type": "genomic", "axis": "right"}, | |
"color": { | |
"field": "value", | |
"type": "quantitative", | |
"range": "warm" | |
}, | |
"width": 600, | |
"height": 570 | |
} | |
] | |
}, | |
{ | |
"tracks": [ | |
{ | |
"title": "Epilogos (hg38)", | |
"data": { | |
"url": "https://higlass.io/api/v1/tileset_info/?d=WtBJUYawQzS9M2WVIIHnlA", | |
"type": "multivec", | |
"row": "category", | |
"column": "position", | |
"value": "value", | |
"categories": [ | |
"Active TSS", | |
"Flanking Active TSS", | |
"Transcr at gene 5\\' and 3\\'", | |
"Strong transcription", | |
"Weak transcription", | |
"Genic enhancers", | |
"Enhancers", | |
"ZNF genes & repeats", | |
"Heterochromatin", | |
"Bivalent/Poised TSS", | |
"Flanking Bivalent TSS/Enh", | |
"Bivalent Enhancer", | |
"Repressed PolyComb", | |
"Weak Repressed PolyComb", | |
"Quiescent/Low" | |
], | |
"binSize": 8 | |
}, | |
"dataTransform": { | |
"filter": [{"field": "value", "inRange": [0, 999999]}] | |
}, | |
"mark": "bar", | |
"x": {"field": "start", "type": "genomic", "axis": "none"}, | |
"xe": {"field": "end", "type": "genomic"}, | |
"y": {"field": "value", "type": "quantitative"}, | |
"color": { | |
"field": "category", | |
"type": "nominal", | |
"range": [ | |
"#FF0000", | |
"#FF4500", | |
"#32CD32", | |
"#008000", | |
"#006400", | |
"#C2E105", | |
"#FFFF00", | |
"#66CDAA", | |
"#8A91D0", | |
"#CD5C5C", | |
"#E9967A", | |
"#BDB76B", | |
"#808080", | |
"#C0C0C0", | |
"#EEEEEE" | |
] | |
}, | |
//"strokeWidth": {"value": 0.5}, | |
//"style": {"outline": "gray"}, | |
"width": 570, | |
"height": 40 | |
} | |
] | |
} | |
] | |
}, | |
{ | |
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"column": "position", | |
"value": "peak" | |
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"title": "HFFc6_H3K4me3", | |
"mark": "bar", | |
"x": {"field": "position", "type": "genomic", "axis": "none"}, | |
"y": {"field": "peak", "type": "quantitative"}, | |
"color": {"value": "darkgreen"}, | |
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"height": 40 | |
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{ | |
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"type": "vector", | |
"column": "position", | |
"value": "peak" | |
}, | |
"title": "HFFc6_ATAC", | |
"mark": "bar", | |
"x": {"field": "position", "type": "genomic"}, | |
"y": {"field": "peak", "type": "quantitative"}, | |
"color": {"value": "purple"}, | |
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"type": "vector", | |
"column": "position", | |
"value": "peak" | |
}, | |
"mark": "bar", | |
"x": {"field": "position", "type": "genomic"}, | |
"y": {"field": "peak", "type": "quantitative"}, | |
"color": {"value": "blue"} | |
}, | |
{ | |
"data": { | |
"url": "https://higlass.io/api/v1/tileset_info/?d=EkPGY0iFQx6Nq6vdF8CpWA", | |
"type": "beddb", | |
"genomicFields": [ | |
{"index": 1, "name": "start"}, | |
{"index": 2, "name": "end"} | |
], | |
"valueFields": [ | |
{"index": 5, "name": "strand", "type": "nominal"}, | |
{"index": 3, "name": "name", "type": "nominal"} | |
] | |
}, | |
"dataTransform": { | |
"filter": [{"field": "strand", "oneOf": ["+"]}] | |
}, | |
"mark": "triangleRight", | |
"x": {"field": "start", "type": "genomic"}, | |
"size": {"value": 10}, | |
"stroke": {"value": "white"}, | |
"strokeWidth": {"value": 1}, | |
"row": { | |
"field": "strand", | |
"type": "nominal", | |
"domain": ["+", "-"] | |
}, | |
"color": {"value": "red"} | |
}, | |
{ | |
"title": "HFFC6_CTCF", | |
"data": { | |
"url": "https://higlass.io/api/v1/tileset_info/?d=EkPGY0iFQx6Nq6vdF8CpWA", | |
"type": "beddb", | |
"genomicFields": [ | |
{"index": 1, "name": "start"}, | |
{"index": 2, "name": "end"} | |
], | |
"valueFields": [ | |
{"index": 5, "name": "strand", "type": "nominal"}, | |
{"index": 3, "name": "name", "type": "nominal"} | |
] | |
}, | |
"dataTransform": { | |
"filter": [{"field": "strand", "oneOf": ["-"]}] | |
}, | |
"mark": "triangleLeft", | |
"x": {"field": "start", "type": "genomic"}, | |
"stroke": {"value": "white"}, | |
"strokeWidth": {"value": 1}, | |
"size": {"value": 10}, | |
"row": { | |
"field": "strand", | |
"type": "nominal", | |
"domain": ["+", "-"] | |
}, | |
"color": {"value": "green"} | |
} | |
], | |
"style": {"outline": "gray"}, | |
"width": 570, | |
"height": 40 | |
} | |
] | |
}, | |
{ | |
"tracks": [ | |
{ | |
"title": "HFFc6_Hi-C", | |
"data": { | |
"url": "https://resgen.io/api/v1/tileset_info/?d=fkUS2EyvQMqJ9dZBxS6wvw", | |
"type": "matrix" | |
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"mark": "rect", | |
"x": {"field": "position1", "type": "genomic", "axis": "top"}, | |
"y": {"field": "position2", "type": "genomic", "axis": "right"}, | |
"color": { | |
"field": "value", | |
"type": "quantitative", | |
"range": "warm" | |
}, | |
"width": 600, | |
"height": 570 | |
} | |
] | |
}, | |
{ | |
"tracks": [ | |
{ | |
"title": "Epilogos (hg38)", | |
"data": { | |
"url": "https://higlass.io/api/v1/tileset_info/?d=WtBJUYawQzS9M2WVIIHnlA", | |
"type": "multivec", | |
"row": "category", | |
"column": "position", | |
"value": "value", | |
"categories": [ | |
"Active TSS", | |
"Flanking Active TSS", | |
"Transcr at gene 5\\' and 3\\'", | |
"Strong transcription", | |
"Weak transcription", | |
"Genic enhancers", | |
"Enhancers", | |
"ZNF genes & repeats", | |
"Heterochromatin", | |
"Bivalent/Poised TSS", | |
"Flanking Bivalent TSS/Enh", | |
"Bivalent Enhancer", | |
"Repressed PolyComb", | |
"Weak Repressed PolyComb", | |
"Quiescent/Low" | |
], | |
"binSize": 8 | |
}, | |
"dataTransform": { | |
"filter": [{"field": "value", "inRange": [0, 999999]}] | |
}, | |
"mark": "bar", | |
"x": {"field": "start", "type": "genomic", "axis": "none"}, | |
"xe": {"field": "end", "type": "genomic"}, | |
"y": {"field": "value", "type": "quantitative"}, | |
"color": { | |
"field": "category", | |
"type": "nominal", | |
"range": [ | |
"#FF0000", | |
"#FF4500", | |
"#32CD32", | |
"#008000", | |
"#006400", | |
"#C2E105", | |
"#FFFF00", | |
"#66CDAA", | |
"#8A91D0", | |
"#CD5C5C", | |
"#E9967A", | |
"#BDB76B", | |
"#808080", | |
"#C0C0C0", | |
"#EEEEEE" | |
] | |
}, | |
//"strokeWidth": {"value": 0.5}, | |
//"style": {"outline": "gray"}, | |
"width": 570, | |
"height": 40 | |
} | |
] | |
} | |
] | |
} | |
] | |
} |
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