cmap.json

{
  "#": "cmap-js example configuration file (json format)",
  "header" : ": soybean and common bean genomes and genetic maps",
  "attribution" : "data attribution: soybase, LIS",
  "initialView" : [ {
     "source" : "pv_consensus",
     "map" : "Pv02",
     "tracks" :[
        {
          "type": "qtl",
          "title": "seed 1",
          "filters": [
            "QTL_root",
            "QTL_seed",
            "QTL_other-seed"
          ],
          "fillColor": ["yellow"],
          "labelStyle": "block",
          "labelPosition" : -1
        },{
          "type": "qtl",
          "filters": [
            "QTL_seed",
            "QTL_root"
          ],
          "fillColor": ["green","red"],
          "labelStyle": "feature"
        }
      ]
  },{
     "source" : "pv_genome",
     "map" : "phavu.Chr02",
     "tracks" : [{
       "type" : "manhattan",
        "dataId" : "manhattan_test",
        "displayWidth" : 50,
        "maxValue" : 6,
        "width" : 2,
        "rulerMajorMark" : 10,
        "rulerMinorMark" : 2,
        "posField" :"Pos",
        "targetField" : "Chr",
        "pField" : "p",
        "lines" : [
          {
            "value": 5,
            "lineWeight": 3,
            "lineColor": "red"
          },
          {
            "value": 2,
            "lineWeight": 3,
            "lineColor": "blue"
          }
        ]
      }]
    }, {
      "source" : "gm_genome",
      "map" : "glyma.Chr01"
        
    }, {
     "source" : "gm_composite",
     "map" : "D1a",
     "tracks" : [{
        "type" : "qtl",
        "filters":["QTL_other-seed","QTL_root"],
        "fillColor": ["orange","blue"],
        "position":-1
      },{
        "type" : "qtl",
        "filters":["QTL_root"],
        "fillColor": ["red"],
        "position":1
      }
     ]
    }
  ],
  "sources" : [ {
      "id" : "pv_consensus",
      "method": "GET",
      "url": "data/PvConsensus_GaleanoFernandez2011_a.cmap",
      "filters" : [],
      "config": {
        "url" : "config/phavu_genes.json",
        "method":"GET",
        "data":{}
      },
      "linkouts" : [
        {
            "featuretypePattern" : "QTL",
            "url" : "https://legumeinfo.org/feature/Phaseolus/vulgaris/QTL/phavu.${item.id}",
            "text" : "View QTL info at LIS"
        },
        {
            "featuretypePattern" : "^(SSR|SNP|AFLP|STS|RAPD)$",
            "url" : "https://legumeinfo.org/feature/Phaseolus/vulgaris/genetic_marker/${item.id}",
            "text" : "View marker at LIS"
        }
      ]
    }, {
      "id" : "pv_genome",
      "method": "GET",
      "url": "data/phavu.collinearity+genes+markers.cmap",
      "filters" : [],
      "config": {
        "url" : "config/phavu_genes.json",
        "method":"GET",
        "data":{}
      },
      "linkouts" : [
        {
            "featuretype" : "gene",
            "url" : "https://legumeinfo.org/gene_links/${item.id}/json",
            "isLinkingService" : true
        }
      ]
    }, {
      "id" : "gm_genome",
      "method": "GET",
      "url": "data/glyma.collinearity+genes+markers.cmap",
      "filters" : [],
      "config": {
        "method" : "GET",
        "url" : "config/phavu_genes.json"
      },
      "linkouts" : [
        {
            "featuretype" : "gene",
            "url" : "https://legumeinfo.org/gene_links/${item.id}/json",
            "isLinkingService" : true
        }
      ]
    }, {
      "id" : "gm_composite",
      "method": "GET",
      "url" : "data/Soybean-GmComposite2003.cmap",
      "filters" : [],
      "linkouts" : [
        {
            "featuretypePattern" : "QTL",
            "url" : "https://legacy.soybase.org/sbt/search/search_results.php?category=QTLName&search_term=${item.id}",
            "text" : "View QTL info at SoyBase"
        },
        {
            "featuretype" : "SNP",
            "url" : "https://legacy.soybase.org/sbt/search/search_results.php?category=SNP&search_term=${item.id}",
            "text" : "View SNP info at SoyBase"
        },
        {
            "featuretypePattern" : "^(SSR|[AR]FLP|Gene|PCR)$",
            "url" : "https://soybase.org/sbt/search/search_results.php?category=LocusName&search_term=${item.id}",
            "text" : "View Marker info at SoyBase"
        }
      ]
    }, {
      "id" : "manhattan_test",
      "method": "GET",
      "url" : "data/sample2.txt",
      "filters" : []
    }
  ]
}