samplevis.json 23.8 KB
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{
  "width": 600,
  "height": 10,
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  "signals": [
    {
      "name": "amplitude_threshold",
      "init": 5
    },
    {
      "name": "amplitude_pct_threshold",
      "init": 0.5
    },
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    {
      "name": "amplitude_markerpct_threshold",
      "init": 0
    },
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    {
      "name": "orientation_threshold",
      "init": 0
    },
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    {
      "name": "show_negative",
      "init": true
    },
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    {
      "name": "show_other",
      "init": true
    },
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    {
      "name": "sort_str_by_length",
      "init": true
    },
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    {
      "name": "bias_threshold",
      "init": 25
    },
    {
      "name": "filter_marker",
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      "init": ""
    },
    {
      "name": "marker_regex",
      "init": {"expr": "regexp('(?:' + replace(replace(replace(filter_marker, /^ *(.*?) *$/, '$1'), /(^| )=(.*?)(?= |$)/g, '$1^$2$$'), / +/g, ')|(?:') + ')')"},
      "expr": "regexp('(?:' + replace(replace(replace(filter_marker, /^ *(.*?) *$/, '$1'), /(^| )=(.*?)(?= |$)/g, '$1^$2$$'), / +/g, ')|(?:') + ')')"
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    },
    {
      "name": "barwidth",
      "init": 15
    },
    {
      "name": "subgraphoffset",
      "init": 70
    },
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    {
      "name": "max_seq_len",
      "init": 70
    },
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    {
      "name": "clickedAllele",
      "verbose": true,
      "streams": [
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        {
          "type": "@alleleSelector:click[datum.thedatum]",
          "expr": "datum.thedatum"
        }
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      ]
    }
  ],
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  "data": [
    {
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      "name": "raw",
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      "values": "sample_data_file_contents_here",
      "format": {
        "type": "tsv",
        "parse": {
          "forward": "number",
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          "forward_noise": "number",
          "forward_add": "number",
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          "reverse": "number",
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          "reverse_noise": "number",
          "reverse_add": "number",
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          "total": "number",
          "total_noise": "number",
          "total_add": "number"
        }
      },
      "transform": [
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        {
          "type": "filter",
          "test": "test(marker_regex, datum.marker)"
        },
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        {
          "type": "formula",
          "field": "forward_corr",
          "expr": "datum.forward_noise? datum.forward-datum.forward_noise : datum.forward"
        },
        {
          "type": "formula",
          "field": "reverse_corr",
          "expr": "datum.reverse_noise? datum.reverse-datum.reverse_noise : datum.reverse"
        },
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        {
          "type": "formula",
          "field": "total_corr",
          "expr": "datum.total_noise? datum.total-datum.total_noise : datum.total"
        },
        {
          "type": "formula",
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          "field": "forward_added",
          "expr": "datum.forward_add? datum.forward_corr+datum.forward_add : datum.forward_corr"
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        },
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        {
          "type": "formula",
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          "field": "reverse_added",
          "expr": "datum.reverse_add? datum.reverse_corr+datum.reverse_add : datum.reverse_corr"
        },
        {
          "type": "formula",
          "field": "total_added",
          "expr": "datum.total_add? datum.total_corr+datum.total_add : datum.total_corr"
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        }
      ]
    },
    {
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      "name": "aggr",
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      "source": "raw",
      "transform": [
        {
          "type": "aggregate",
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          "groupby": ["marker"],
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          "summarize": {"total_added": ["sum", "max"]}
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        }
      ]
    },
    {
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      "name": "preannotated",
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      "source": "raw",
      "transform": [
        {
          "type": "lookup",
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          "on": "aggr",
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          "onKey": "marker",
          "keys": ["marker"],
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          "as": ["aggr"],
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          "default": {"max_total_added": 0, "sum_total_added": 0}
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        },
        {
          "type": "formula",
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          "field": "pct_of_max",
          "expr": "datum.aggr.max_total_added? (datum.total_added / datum.aggr.max_total_added * 100) : 100"
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        },
        {
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          "type": "formula",
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          "field": "pct_of_sum",
          "expr": "datum.aggr.sum_total_added? (datum.total_added / datum.aggr.sum_total_added * 100) : 100"
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        },
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        {
          "type": "formula",
          "field": "seq_order",
          "expr": "(sort_str_by_length && test(/^CE\\d+\\.?\\d*_/, datum.sequence))? parseFloat(substring(datum.sequence, 2, indexof(datum.sequence, '_'))) : 1/0"
        },
        {
          "type": "sort",
          "by": ["marker", "seq_order", "-total_added", "-total_corr", "-total", "sequence"]
        },
        {
          "type": "rank"
        },
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        {
          "type": "formula",
          "field": "markersequence",
          "expr": "datum.marker + '\t' + datum.sequence"
        }
      ]
    },
    {
      "name": "annotated",
      "source": "preannotated",
      "transform": [
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        {
          "type": "filter",
          "test": "datum.sequence != 'Other sequences'"
        },
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        {
          "type": "formula",
          "field": "shared",
          "expr": "max(0, datum.total_corr)"
        },
        {
          "type": "formula",
          "field": "corr_shared",
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          "expr": "min(datum.total, datum.total_added)"
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        },
        {
          "type": "formula",
          "field": "corr_decreased",
          "expr": "max(datum.total, datum.corr_shared)"
        },
        {
          "type": "formula",
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          "field": "forwardpct",
          "expr": "datum.total_added? (100.0 / datum.total_added * datum.forward_added) : 50"
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        },
        {
          "type": "formula",
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          "field": "minimum",
          "expr": "min(0, datum.total_corr)"
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        },
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        {
          "type": "formula",
          "field": "xlow",
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          "expr": "datum.minimum*1.05"
        },
        {
          "type": "formula",
          "field": "maximum",
          "expr": "max(datum.total, datum.total_added)"
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        },
        {
          "type": "formula",
          "field": "xhigh",
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          "expr": "datum.maximum*1.05"
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        },
        {
          "type": "formula",
          "field": "biasmark",
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          "expr": "50-abs(datum.forwardpct-50) < bias_threshold? '\u2605' : ''"
        },
        {
          "type": "formula",
          "field": "thedatum",
          "expr": "datum"
        }
      ]
    },
    {
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      "name": "table",
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      "source": "preannotated",
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      "transform": [
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        {
          "type": "formula",
          "field": "sequence",
          "expr": "((show_negative? abs(datum.total_added) : datum.total_added) >= amplitude_threshold && (show_negative? abs(datum.pct_of_max) : datum.pct_of_max) >= amplitude_pct_threshold && (show_negative? abs(datum.pct_of_sum) : datum.pct_of_sum) >= amplitude_markerpct_threshold && min(show_negative? abs(datum.forward_added) : datum.forward_added, show_negative? abs(datum.reverse_added) : datum.reverse_added) >= orientation_threshold)? datum.sequence : 'Other sequences'"
        },
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        {
          "type": "filter",
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          "test": "show_other || datum.sequence != 'Other sequences'"
        },
        {
          "type": "aggregate",
          "groupby": ["marker", "sequence"],
          "summarize": [
            {"field": "forward",        "ops": ["sum"], "as": ["forward"]},
            {"field": "reverse",        "ops": ["sum"], "as": ["reverse"]},
            {"field": "total",          "ops": ["sum"], "as": ["total"]},
            {"field": "forward_noise",  "ops": ["sum"], "as": ["forward_noise"]},
            {"field": "reverse_noise",  "ops": ["sum"], "as": ["reverse_noise"]},
            {"field": "total_noise",    "ops": ["sum"], "as": ["total_noise"]},
            {"field": "forward_add",    "ops": ["sum"], "as": ["forward_add"]},
            {"field": "reverse_add",    "ops": ["sum"], "as": ["reverse_add"]},
            {"field": "total_add",      "ops": ["sum"], "as": ["total_add"]},
            {"field": "forward_corr",   "ops": ["sum"], "as": ["forward_corr"]},
            {"field": "reverse_corr",   "ops": ["sum"], "as": ["reverse_corr"]},
            {"field": "total_corr",     "ops": ["sum"], "as": ["total_corr"]},
            {"field": "forward_added",  "ops": ["sum"], "as": ["forward_added"]},
            {"field": "reverse_added",  "ops": ["sum"], "as": ["reverse_added"]},
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            {"field": "total_added",    "ops": ["sum"], "as": ["total_added"]},
            {"field": "rank",           "ops": ["min"], "as": ["rank"]}
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          ]
        },
        {
          "type": "formula",
          "field": "shared",
          "expr": "max(0, datum.total_corr)"
        },
        {
          "type": "formula",
          "field": "corr_shared",
          "expr": "min(datum.total, datum.total_added)"
        },
        {
          "type": "formula",
          "field": "corr_decreased",
          "expr": "max(datum.total, datum.corr_shared)"
        },
        {
          "type": "formula",
          "field": "forwardpct",
          "expr": "datum.total_added? (100.0 / datum.total_added * datum.forward_added) : 50"
        },
        {
          "type": "formula",
          "field": "minimum",
          "expr": "min(0, datum.total_corr)"
        },
        {
          "type": "formula",
          "field": "xlow",
          "expr": "datum.minimum*1.05"
        },
        {
          "type": "formula",
          "field": "maximum",
          "expr": "max(datum.total, datum.total_added)"
        },
        {
          "type": "formula",
          "field": "xhigh",
          "expr": "datum.maximum*1.05"
        },
        {
          "type": "formula",
          "field": "biasmark",
          "expr": "50-abs(datum.forwardpct-50) < bias_threshold? '\u2605' : ''"
        },
        {
          "type": "formula",
          "field": "markersequence",
          "expr": "datum.marker + '\t' + datum.sequence"
        },
        {
          "type": "lookup",
          "on": "annotated",
          "onKey": "markersequence",
          "keys": ["markersequence"],
          "as": ["thedatum"]
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        },
        {
          "type": "formula",
          "field": "rank",
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          "expr": "datum.sequence == 'Other sequences'? 1/0 : datum.rank"
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        },
        {
          "type": "formula",
          "field": "sequence_disp",
          "expr": "length(datum.sequence) > max_seq_len+1? substring(datum.sequence, 0, max_seq_len) + '\u2026' : datum.sequence"
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        }
      ]
    },
    {
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      "name": "barcounts",
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      "source": "table",
      "transform": [
        {
          "type": "aggregate",
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          "groupby": ["marker"],
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          "summarize": {"*": "count"}
        }
      ]
    },
    {
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      "name": "subgraphpadding",
      "source": "barcounts",
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      "transform": [
        {
          "type": "cross",
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          "diagonal": false,
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          "filter": "datum.b.marker < datum.a.marker"
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        },
        {
          "type": "formula",
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          "field": "marker",
          "expr": "datum.a.marker"
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        },
        {
          "type": "aggregate",
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          "groupby": ["marker"],
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          "summarize": [{"field": "*", "ops": ["count"], "as": ["cumulpadding"]}]
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        }
      ]
    },
    {
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      "name": "subgraphoffsets",
      "source": "barcounts",
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      "transform": [
        {
          "type": "cross",
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          "with": "table",
          "diagonal": false,
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          "filter": "datum.b.marker < datum.a.marker"
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        },
        {
          "type": "formula",
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          "field": "marker",
          "expr": "datum.a.marker"
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        },
        {
          "type": "aggregate",
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          "groupby": ["marker"],
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          "summarize": [{"field": "*", "ops": ["count"], "as": ["cumulcount"]}]
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        }
      ]
    },
    {
      "name": "yscale",
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      "source": "barcounts",
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      "transform": [
        {
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          "type": "lookup",
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          "on": "subgraphpadding",
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          "onKey": "marker",
          "keys": ["marker"],
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          "as": ["paddingobj"],
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          "default": {"cumulpadding": 0}
        },
        {
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          "type": "lookup",
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          "on": "subgraphoffsets",
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          "onKey": "marker",
          "keys": ["marker"],
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          "as": ["offsetobj"],
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          "default": {"cumulcount": 0}
        },
        {
          "type": "formula",
          "field": "offset",
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          "expr": "barwidth*datum.offsetobj.cumulcount + subgraphoffset*datum.paddingobj.cumulpadding"
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        },
        {
          "type": "formula",
          "field": "end",
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          "expr": "datum.offset + barwidth*datum.count"
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        }
      ]
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    },
    {
      "name": "selectedAlleles",
      "modify": [
        {
          "type": "toggle",
          "signal": "clickedAllele",
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          "field": "thedatum"
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        }
      ]
    }
  ],
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  "scales": [
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    {
      "name": "b",
      "type": "ordinal",
      "range": ["black", "red"],
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      "domain": ["", "\u2605"]
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    },
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    {
      "name": "c",
      "type": "ordinal",
      "range": ["#5e3c99", "#b2abd2", "#fdb863", "#e66101"],
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      "domain": ["Genuine reads", "Noise reads", "Noise/recovered overlap", "Recovered reads"]
    },
    {
      "name": "d",
      "type": "ordinal",
      "range": ["transparent"],
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      "domain": ["\u2014 Strand balance"]
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    }
  ],
  "marks": [
    {
      "type": "text",
      "from": {
        "data": "yscale"
      },
      "properties": {
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        "update": {
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          "x": {"field": {"group": "width"}, "mult": 0.5},
          "y": {"field": "offset"},
          "fontWeight": {"value": "bold"},
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          "text": {"field": "marker"},
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          "align": {"value": "center"},
          "baseline": {"value": "bottom"},
          "fill": {"value": "black"}
        }
      }
    },
    {
      "type": "group",
      "from": {
        "data": "table",
        "transform": [
          {
            "type": "facet",
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            "groupby": ["marker"]
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          },
          {
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            "type": "lookup",
            "on": "yscale",
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            "onKey": "marker",
            "keys": ["marker"],
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            "as": ["subgraphscale"]
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          }
        ]
      },
      "properties": {
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        "update": {
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          "x": {"value": 0},
          "width": {"field": {"group": "width"}},
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          "y": {"field": "subgraphscale.offset"},
          "y2": {"field": "subgraphscale.end"},
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          "stroke": {"value": "#dddddd"}
        }
      },
      "scales": [
        {
          "name": "x",
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          "type": "linear",
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          "nice": true,
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          "range": "width",
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          "domain": {"field": ["xlow", "xhigh"]}
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        },
        {
          "name": "y",
          "type": "ordinal",
          "range": "height",
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          "domain": {"field": "sequence", "sort": {"field": "rank", "op": "min"}}
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        }
      ],
      "axes": [
        {
          "type": "x",
          "scale": "x",
          "grid": true,
          "layer": "back",
          "title": "Number of reads",
          "properties": {
            "labels": {
              "align": {"value": "right"},
              "baseline": {"value": "middle"},
              "dy": {"value": 3},
              "angle": {"value": -25}
            }
          }
        },
        {
          "type": "y",
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          "scale": "y",
          "properties": {
            "labels": {
              "fill": {"value": "transparent"}
            }
          }
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        }
      ],
      "legends": [
        {
          "fill": "c",
          "properties": {
            "symbols": {
              "size": {"value": 100},
              "stroke": {"value": "transparent"},
              "fillOpacity": {"value": 0.8}
            }
          }
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        },
        {
          "fill": "d",
          "properties": {
            "symbols": {
              "stroke": {"value": "transparent"}
            },
            "labels": {
              "x": {"value": 2}
            }
          }
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        }
      ],
      "marks": [
        {
          "type": "rect",
          "properties": {
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            "update": {
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              "x": [
                {"test": "datum.thedatum", "scale": "x", "value": 0},
                {"scale": "x", "value": 0, "offset": 0.5}
              ],
              "x2": [
                {"test": "datum.thedatum", "scale": "x", "field": "shared"},
                {"scale": "x", "field": "shared", "offset": -0.5}
              ],
              "y": [
                {"test": "datum.thedatum", "scale": "y", "field": "sequence", "offset": 1},
                {"scale": "y", "field": "sequence", "offset": 1.5}
              ],
              "height": [
                {"test": "datum.thedatum", "scale": "y", "band": true, "offset": -2},
                {"scale": "y", "band": true, "offset": -3}
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