{
  "version": "1.0.18",
  "name": "chr19 · how the liver handles cholesterol — HepG2 rE2G elements",
  "description": "HepG2 ENCODE rE2G ENCFF960GTR / ENCSR411RGL, GRCh38 chr19. Companion to the supplied Gosling cholesterol windows and colors. Scores are predicted rE2G link scores (0 = unreported link), not expression. ClinVar counts are positional overlaps ([POS-1, POS-1+len(REF))) with clinvar_hg38_all.vcf.gz and do not establish regulatory effects. CYP2A6 is absent from this matrix; its supplied locus window contains no elements.",
  "initStrategy": "auto",
  "datasets": [
    {
      "uid": "HepG2",
      "name": "HepG2 ENCFF960GTR chr19",
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          "url": "https://users.abdenlab.org/voy/vitessce_cvh/hepg2_sci/chr19/chr19.matrix.csv",
          "coordinationValues": {
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            "featureType": "gene",
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          }
        },
        {
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          "url": "https://users.abdenlab.org/voy/vitessce_cvh/hepg2_sci/chr19/chr19.ccre_metadata.csv",
          "coordinationValues": {
            "obsType": "element",
            "obsLabelsType": "Overlapping cCREs (ID: class)"
          },
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            "obsLabels": "ccre_id_class"
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          "coordinationValues": {
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          },
          "options": {
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            "obsLabels": "ccre_count"
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        },
        {
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        },
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            "featureType": "ClinVar annotation",
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        },
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          },
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        },
        {
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            "obsLabelsType": "Overlapping ClinVar variants"
          },
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            "obsLabels": "clinvar_details"
          }
        },
        {
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          "url": "https://users.abdenlab.org/voy/vitessce_cvh/hepg2_sci/chr19/chr19.map.embedding.csv",
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            "embeddingType": "Chromosome map"
          },
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          }
        },
        {
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            "obsType": "element",
            "embeddingType": "Link landscape"
          },
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        },
        {
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        }
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    },
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    },
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          ]
        },
        {
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            "linked to LDLR"
          ],
          "color": [
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          ]
        },
        {
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          ],
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          ],
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          ]
        },
        {
          "path": [
            "ClinVar overlap",
            "With ClinVar overlap"
          ],
          "color": [
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            140,
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          ]
        },
        {
          "path": [
            "ClinVar overlap",
            "No ClinVar overlap"
          ],
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            110,
            110,
            110
          ]
        }
      ]
    },
    "obsColorEncoding": {
      "A": "cellSetSelection"
    },
    "embeddingType": {
      "map": "Chromosome map",
      "land": "Link landscape"
    },
    "embeddingObsSetLabelsVisible": {
      "map": false,
      "land": true
    },
    "embeddingObsSetPolygonsVisible": {
      "A": false
    },
    "embeddingObsRadiusMode": {
      "A": "manual"
    },
    "embeddingObsRadius": {
      "map": 3,
      "land": 2
    },
    "embeddingObsOpacityMode": {
      "A": "auto"
    },
    "heatmapZoomX": {
      "rows": 0
    },
    "heatmapZoomY": {
      "rows": 0
    },
    "heatmapTargetY": {
      "rows": 0
    },
    "heatmapTargetX": {
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      "classes": 0,
      "clinvar": 0
    },
    "featureValueColormap": {
      "scores": "plasma",
      "classes": "plasma",
      "clinvar": "plasma"
    },
    "featureValueColormapRange": {
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      ],
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      ],
      "clinvar": [
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  },
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    {
      "component": "description",
      "coordinationScopes": {
        "dataset": "A",
        "obsType": "A"
      },
      "props": {
        "title": "chr19 · how the liver handles cholesterol",
        "description": "**HepG2 predicted regulatory links on chr19** — companion to the four Gosling windows and colors.\n\nEach dot is one rE2G element. **Chromosome map:** x = midpoint (Mb); height = log₂(1 + ClinVar count), scaled. **Link landscape:** UMAP of normalized gene-score profiles; proximity indicates similar predicted targets.\n\nClick a gene to color both maps by its link score and update the violin. Select element sets to return to set colors and filter the heatmaps. The dot plot uses LDLR, APOE and TM6SF2 (full feature IDs).\n\n**Source limitation:** CYP2A6 is absent from this matrix and the supplied CYP2A6–2B6 locus contains no elements. Its ±1 Mb neighborhood remains available. Missing data do not imply zero biological activity.\n\nScores are links, not expression; ClinVar overlaps do not establish regulatory effects. Gosling correspondence is by windows/colors, not automatic cross-application synchronization.",
        "descriptionType": "markdown"
      },
      "x": 0,
      "y": 0,
      "w": 3,
      "h": 4
    },
    {
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        "obsSetExpansion": "A",
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        "embeddingObsSetLabelsVisible": "map",
        "embeddingObsSetPolygonsVisible": "A",
        "embeddingObsRadiusMode": "A",
        "embeddingObsRadius": "map",
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        "featureValueColormap": "scores",
        "featureValueColormapRange": "scores",
        "obsLabelsType": [
          "clinvar_count",
          "ccre_matches"
        ]
      },
      "props": {
        "title": "Chromosome map · position on chr19 × ClinVar burden",
        "observationsLabelOverride": "element"
      },
      "x": 3,
      "y": 0,
      "w": 6,
      "h": 4
    },
    {
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        "embeddingObsSetLabelsVisible": "land",
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        "embeddingObsRadius": "land",
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        "featureValueColormap": "scores",
        "featureValueColormapRange": "scores",
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        ]
      },
      "props": {
        "title": "Link landscape · similar predicted targets",
        "observationsLabelOverride": "element"
      },
      "x": 9,
      "y": 0,
      "w": 3,
      "h": 4
    },
    {
      "component": "heatmap",
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        "featureHighlight": "classes",
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        "heatmapZoomX": "rows",
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        "heatmapTargetY": "rows",
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        "featureValueColormap": "classes",
        "featureValueColormapRange": "classes",
        "obsColorEncoding": "A"
      },
      "props": {
        "transpose": false,
        "title": "cCRE class",
        "observationsLabelOverride": "regulatory element",
        "variablesLabelOverride": "cCRE class"
      },
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    },
    {
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        "featureHighlight": "clinvar",
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        "heatmapTargetY": "rows",
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        "featureValueColormap": "clinvar",
        "featureValueColormapRange": "clinvar",
        "obsColorEncoding": "A"
      },
      "props": {
        "transpose": false,
        "title": "ClinVar records",
        "observationsLabelOverride": " ",
        "variablesLabelOverride": "ClinVar annotation"
      },
      "x": 2,
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      "h": 5
    },
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        "featureValueColormapRange": "scores",
        "obsColorEncoding": "A"
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      "props": {
        "transpose": false,
        "title": "rE2G link score · element × gene",
        "observationsLabelOverride": " "
      },
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    },
    {
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      },
      "props": {
        "title": "Element sets"
      },
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    },
    {
      "component": "featureList",
      "coordinationScopes": {
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      },
      "props": {
        "title": "Genes",
        "variablesLabelOverride": "gene"
      },
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    },
    {
      "component": "dotPlot",
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      },
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        "transpose": false
      },
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    },
    {
      "component": "obsSetFeatureValueDistribution",
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      },
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      },
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}
