verySimpleExample.json

gistfile1.txt

{
    "title": "IslandViewer 4 (Bertelli et al. 2017)",
    "subtitle": "Salmonella enterica subsp. enterica serovar Typhi Ty2, complete genome.",
    "description": "Reimplementation of https://www.pathogenomics.sfu.ca/islandviewer/accession/NC_004631.1/",
    "assembly": [
        [
            "NC_004631.1",
            4791961
        ]
    ],
    "spacing": 50,
    "views": [
        {
            "layout": "circular",
            "static": true,
            "alignment": "overlay",
            "spacing": 0.1,
            "tracks": [
                {
                    "data": {
                        "url": "https://s3.amazonaws.com/gosling-lang.org/data/IslandViewer/NC_004631.1_GCcontent.csv",
                        "type": "csv",
                        "separator": "\t",
                        "genomicFields": [
                            "Position"
                        ]
                    },
                    "id": "first",
                    "y": {
                        "field": "GCcontent",
                        "type": "quantitative",
                        "range": [
                            -250,
                            0
                        ],
                        "axis": "none"
                    },
                    "mark": "line",
                    "size": {
                        "value": 0.5
                    },
                    "x": {
                        "field": "Position",
                        "type": "genomic"
                    },
                    "color": {
                        "value": "black"
                    }
                },
                {
                    "experimental": {
                        "mouseEvents": true
                    },
                    "style": {
                        "outlineWidth": 1,
                        "outline": "black"
                    },
                    "id": "second",
                    "data": {
                        "url": "https://s3.amazonaws.com/gosling-lang.org/data/IslandViewer/NC_004631.1_annotations.csv",
                        "type": "csv",
                        "genomicFields": [
                            "Gene start"
                        ]
                    },
                    "dataTransform": [
                        {
                            "type": "displace",
                            "method": "pile",
                            "boundingBox": {
                                "padding": 3.5,
                                "startField": "Gene start",
                                "endField": "Gene start"
                            },
                            "newField": "row"
                        }
                    ],
                    "y": {
                        "field": "row",
                        "type": "nominal",
                        "flip": true
                    },
                    "mark": "point",
                    "x": {
                        "field": "Gene start",
                        "type": "genomic"
                    },
                    "size": {
                        "value": 3
                    },
                    "color": {
                        "field": "Type",
                        "type": "nominal",
                        "domain": [
                            "Victors",
                            "BLAST",
                            "RGI",
                            "PAG"
                        ],
                        "range": [
                            "#460B80",
                            "#A684EA",
                            "#FF9CC1",
                            "#FF9CC1"
                        ]
                    }
                },
                {
                    "data": {
                        "type": "csv",
                        "url": "https://s3.amazonaws.com/gosling-lang.org/data/IslandViewer/NC_004631.1_islands.csv",
                        "chromosomeField": "Accession",
                        "genomicFields": [
                            "Island start",
                            "Island end"
                        ]
                    },
                    "x": {
                        "field": "Island start",
                        "type": "genomic"
                    },
                    "xe": {
                        "field": "Island end",
                        "type": "genomic"
                    },
                    "id": "third",
                    "row": {
                        "field": "Method",
                        "domain": [
                            "Predicted by at least one method",
                            "IslandPath-DIMOB",
                            "SIGI-HMM",
                            "IslandPick",
                            "Islander"
                        ],
                        "type": "nominal"
                    },
                    "color": {
                        "field": "Method",
                        "type": "nominal",
                        "domain": [
                            "Predicted by at least one method",
                            "IslandPath-DIMOB",
                            "SIGI-HMM",
                            "IslandPick",
                            "Islander"
                        ],
                        "range": [
                            "#B22222",
                            "#4169E1",
                            "#FF8C00",
                            "#008001",
                            "#40E0D0"
                        ]
                    },
                    "mark": "rect"
                },
                {
                    "mark": "brush",
                    "id": "brush",
                    "x": {
                        "linkingId": "detail"
                    }
                }
            ],
            "width": 400,
            "centerRadius": 0.5
        }
    ]
}