{
  "$schema": "https://pivograph.com/schemas/project/v1.json",
  "format": "pivograph-project",
  "schemaVersion": 1,
  "generator": {
    "name": "PivoGraph",
    "version": "1.4.0",
    "url": "https://pivograph.com"
  },
  "createdAt": "2026-09-18T16:11:31.257Z",
  "modifiedAt": "2026-09-18T16:11:31.257Z",
  "meta": {
    "title": "KEGG Pathway Enrichment Bubble Plot",
    "description": "KEGG pathway enrichment for a synthetic set of differentially expressed tumor-cell genes after treatment. Rich factor and −log10 P set position, hit count sets bubble area, and pathway class sets color; size-legend labels are illustrative rounded values.",
    "authors": [
      "PivoGraph"
    ],
    "license": "CC0-1.0",
    "source": "Synthetic data generated for this example"
  },
  "view": {
    "activeTableId": "ds-959976ab-7ba2-4811-b4c8-357b4db91365",
    "workspaceView": "graph"
  },
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      "name": "KEGG pathway enrichment",
      "format": "multipleVariables",
      "replicates": 1,
      "dataSets": [
        {
          "name": "Pathway",
          "title": "Pathway",
          "values": [
            [
              "Endocytosis"
            ],
            [
              "Lysosome"
            ],
            [
              "Gap junction"
            ],
            [
              "MAPK signaling"
            ],
            [
              "Starch and sucrose metabolism"
            ],
            [
              "Th1/Th2 differentiation"
            ],
            [
              "Antigen processing and presentation"
            ],
            [
              "T cell receptor signaling"
            ],
            [
              "Glycolysis"
            ],
            [
              "Peroxisome"
            ],
            [
              "Th17 cell differentiation"
            ],
            [
              "RIG-I-like receptor"
            ],
            [
              "Hippo signaling"
            ],
            [
              "Notch signaling"
            ],
            [
              "HIF-1 signaling"
            ],
            [
              "Adherens junction"
            ],
            [
              "p53 signaling"
            ],
            [
              "Oxidative phosphorylation"
            ],
            [
              "Sphingolipid metabolism"
            ],
            [
              "Phagosome"
            ],
            [
              "Cell cycle"
            ],
            [
              "Cytosolic DNA-sensing"
            ],
            [
              "FoxO signaling"
            ],
            [
              "Chemokine signaling"
            ],
            [
              "Leukocyte migration"
            ],
            [
              "cAMP signaling"
            ],
            [
              "Necroptosis"
            ],
            [
              "Purine metabolism"
            ],
            [
              "Sphingolipid signaling"
            ],
            [
              "Wnt signaling"
            ],
            [
              "Focal adhesion"
            ],
            [
              "Rap1 signaling"
            ],
            [
              "B cell receptor signaling"
            ],
            [
              "Glutathione metabolism"
            ],
            [
              "mTOR signaling"
            ],
            [
              "Intestinal immune network"
            ],
            [
              "IL-17 signaling pathway"
            ],
            [
              "ECM-receptor interaction"
            ],
            [
              "Apoptosis"
            ],
            [
              "Ras signaling"
            ],
            [
              "Phospholipase D signaling"
            ],
            [
              "Inositol phosphate metabolism"
            ],
            [
              "Toll-like receptor"
            ],
            [
              "NF-kappa B signaling"
            ],
            [
              "Autophagy"
            ],
            [
              "Pyrimidine metabolism"
            ],
            [
              "Arachidonic acid metabolism"
            ],
            [
              "NOD-like receptor signaling"
            ],
            [
              "TNF signaling pathway"
            ],
            [
              "ErbB signaling"
            ],
            [
              "Tight junction"
            ],
            [
              "Fatty acid degradation"
            ],
            [
              "Glycerolipid metabolism"
            ],
            [
              "Hedgehog signaling"
            ],
            [
              "Ferroptosis"
            ],
            [
              "Pyruvate metabolism"
            ],
            [
              "Retinol metabolism"
            ],
            [
              "PI3K-Akt signaling"
            ],
            [
              "TCA cycle"
            ],
            [
              "Amino sugar metabolism"
            ]
          ]
        },
        {
          "name": "Category",
          "title": "Category",
          "values": [
            [
              "Cellular Processes"
            ],
            [
              "Cellular Processes"
            ],
            [
              "Cellular Processes"
            ],
            [
              "Growth & Survival"
            ],
            [
              "Metabolism"
            ],
            [
              "Immunity"
            ],
            [
              "Immunity"
            ],
            [
              "Immunity"
            ],
            [
              "Metabolism"
            ],
            [
              "Cellular Processes"
            ],
            [
              "Immunity"
            ],
            [
              "Immunity"
            ],
            [
              "Growth & Survival"
            ],
            [
              "Growth & Survival"
            ],
            [
              "Cellular Processes"
            ],
            [
              "Cellular Processes"
            ],
            [
              "Growth & Survival"
            ],
            [
              "Metabolism"
            ],
            [
              "Metabolism"
            ],
            [
              "Cellular Processes"
            ],
            [
              "Cellular Processes"
            ],
            [
              "Immunity"
            ],
            [
              "Growth & Survival"
            ],
            [
              "Immunity"
            ],
            [
              "Immunity"
            ],
            [
              "Cellular Processes"
            ],
            [
              "Cellular Processes"
            ],
            [
              "Metabolism"
            ],
            [
              "Growth & Survival"
            ],
            [
              "Growth & Survival"
            ],
            [
              "Cellular Processes"
            ],
            [
              "Growth & Survival"
            ],
            [
              "Immunity"
            ],
            [
              "Metabolism"
            ],
            [
              "Growth & Survival"
            ],
            [
              "Immunity"
            ],
            [
              "Immunity"
            ],
            [
              "Cellular Processes"
            ],
            [
              "Growth & Survival"
            ],
            [
              "Growth & Survival"
            ],
            [
              "Growth & Survival"
            ],
            [
              "Metabolism"
            ],
            [
              "Immunity"
            ],
            [
              "Immunity"
            ],
            [
              "Cellular Processes"
            ],
            [
              "Metabolism"
            ],
            [
              "Metabolism"
            ],
            [
              "Immunity"
            ],
            [
              "Immunity"
            ],
            [
              "Growth & Survival"
            ],
            [
              "Cellular Processes"
            ],
            [
              "Metabolism"
            ],
            [
              "Metabolism"
            ],
            [
              "Growth & Survival"
            ],
            [
              "Cellular Processes"
            ],
            [
              "Metabolism"
            ],
            [
              "Metabolism"
            ],
            [
              "Growth & Survival"
            ],
            [
              "Metabolism"
            ],
            [
              "Metabolism"
            ]
          ]
        },
        {
          "name": "Rich_Factor",
          "title": "Rich_Factor",
          "values": [
            [
              0.47
            ],
            [
              0.13
            ],
            [
              0.16
            ],
            [
              0.16
            ],
            [
              0.48
            ],
            [
              0.3
            ],
            [
              0.26
            ],
            [
              0.45
            ],
            [
              0.41
            ],
            [
              0.38
            ],
            [
              0.16
            ],
            [
              0.19
            ],
            [
              0.17
            ],
            [
              0.26
            ],
            [
              0.17
            ],
            [
              0.25
            ],
            [
              0.23
            ],
            [
              0.45
            ],
            [
              0.69
            ],
            [
              0.54
            ],
            [
              0.18
            ],
            [
              0.73
            ],
            [
              0.17
            ],
            [
              0.43
            ],
            [
              0.6
            ],
            [
              0.37
            ],
            [
              0.67
            ],
            [
              0.26
            ],
            [
              0.2
            ],
            [
              0.17
            ],
            [
              0.12
            ],
            [
              0.64
            ],
            [
              0.28
            ],
            [
              0.15
            ],
            [
              0.35
            ],
            [
              0.24
            ],
            [
              0.25
            ],
            [
              0.4
            ],
            [
              0.74
            ],
            [
              0.24
            ],
            [
              0.39
            ],
            [
              0.4
            ],
            [
              0.13
            ],
            [
              0.44
            ],
            [
              0.62
            ],
            [
              0.41
            ],
            [
              0.23
            ],
            [
              0.16
            ],
            [
              0.29
            ],
            [
              0.71
            ],
            [
              0.73
            ],
            [
              0.52
            ],
            [
              0.61
            ],
            [
              0.5
            ],
            [
              0.5
            ],
            [
              0.33
            ],
            [
              0.37
            ],
            [
              0.17
            ],
            [
              0.28
            ],
            [
              0.24
            ]
          ]
        },
        {
          "name": "negLog10P",
          "title": "negLog10P",
          "values": [
            [
              18.8
            ],
            [
              3.7
            ],
            [
              7
            ],
            [
              6.8
            ],
            [
              19.1
            ],
            [
              15
            ],
            [
              14
            ],
            [
              18.2
            ],
            [
              18.7
            ],
            [
              17.1
            ],
            [
              6.8
            ],
            [
              10
            ],
            [
              8.5
            ],
            [
              12.5
            ],
            [
              7
            ],
            [
              15.5
            ],
            [
              13.9
            ],
            [
              18.6
            ],
            [
              19.1
            ],
            [
              19.3
            ],
            [
              10.5
            ],
            [
              19.8
            ],
            [
              8.9
            ],
            [
              19.8
            ],
            [
              18.3
            ],
            [
              17.5
            ],
            [
              19.8
            ],
            [
              18.2
            ],
            [
              11.6
            ],
            [
              7.2
            ],
            [
              2.9
            ],
            [
              19.8
            ],
            [
              13.9
            ],
            [
              6.1
            ],
            [
              17.2
            ],
            [
              10.9
            ],
            [
              11.4
            ],
            [
              18.8
            ],
            [
              17
            ],
            [
              11.7
            ],
            [
              18.8
            ],
            [
              19.3
            ],
            [
              1.5
            ],
            [
              13.2
            ],
            [
              19.8
            ],
            [
              19.8
            ],
            [
              11.9
            ],
            [
              1.5
            ],
            [
              17.6
            ],
            [
              15.1
            ],
            [
              19.8
            ],
            [
              18.9
            ],
            [
              17.3
            ],
            [
              16.5
            ],
            [
              18.2
            ],
            [
              13.7
            ],
            [
              19.1
            ],
            [
              9.5
            ],
            [
              16.3
            ],
            [
              13.7
            ]
          ]
        },
        {
          "name": "Gene_Count",
          "title": "Gene_Count",
          "values": [
            [
              123
            ],
            [
              121
            ],
            [
              109
            ],
            [
              105
            ],
            [
              104
            ],
            [
              102
            ],
            [
              102
            ],
            [
              101
            ],
            [
              91
            ],
            [
              78
            ],
            [
              73
            ],
            [
              72
            ],
            [
              72
            ],
            [
              71
            ],
            [
              67
            ],
            [
              67
            ],
            [
              58
            ],
            [
              52
            ],
            [
              45
            ],
            [
              43
            ],
            [
              35
            ],
            [
              34
            ],
            [
              34
            ],
            [
              33
            ],
            [
              32
            ],
            [
              32
            ],
            [
              31
            ],
            [
              29
            ],
            [
              29
            ],
            [
              27
            ],
            [
              27
            ],
            [
              26
            ],
            [
              24
            ],
            [
              23
            ],
            [
              23
            ],
            [
              22
            ],
            [
              18
            ],
            [
              18
            ],
            [
              17
            ],
            [
              17
            ],
            [
              17
            ],
            [
              16
            ],
            [
              16
            ],
            [
              15
            ],
            [
              15
            ],
            [
              14
            ],
            [
              14
            ],
            [
              14
            ],
            [
              14
            ],
            [
              14
            ],
            [
              14
            ],
            [
              13
            ],
            [
              13
            ],
            [
              13
            ],
            [
              13
            ],
            [
              12
            ],
            [
              12
            ],
            [
              11
            ],
            [
              10
            ],
            [
              10
            ]
          ]
        }
      ],
      "graph": {
        "variantId": "mv-bubble",
        "plot": {
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            "kind": "bubble",
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              "x": 2,
              "y": 3,
              "size": 4,
              "color": 1,
              "shape": null,
              "label": null,
              "lower": null,
              "upper": null
            },
            "maxBubbleSize": 12,
            "volcano": {
              "log2FcCutoff": 1,
              "pCutoff": 0.05,
              "yIsNegLog10": false,
              "maxLabels": 20
            },
            "forest": {
              "referenceValue": 1
            }
          }
        },
        "activePresetId": "starry",
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                "color": {
                  "hex": "#323232",
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              }
            },
            "color:s:Growth & Survival": {
              "symbol": {
                "color": {
                  "hex": "#1b6393",
                  "alpha": 1
                }
              }
            },
            "color:s:Immunity": {
              "symbol": {
                "color": {
                  "hex": "#fcd351",
                  "alpha": 1
                }
              }
            },
            "color:s:Metabolism": {
              "symbol": {
                "color": {
                  "hex": "#c7e3cc",
                  "alpha": 1
                }
              }
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          },
          "perPoint": {}
        },
        "graphSettingsOverride": {},
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            "frameStyle": "frameWithTicksInward",
            "majorGrid": {
              "show": true,
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              "thickness": 0.5,
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          "xContinuous": {},
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          "rightY": {},
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          "heightPt": null
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              "label": "Cellular Processes"
            },
            "mv-color:s:Growth & Survival": {
              "label": "Growth & Survival"
            },
            "mv-color:s:Immunity": {
              "label": "Immunity"
            },
            "mv-color:s:Metabolism": {
              "label": "Metabolism"
            },
            "mv-size:0": {
              "label": "n = 10"
            },
            "mv-size:1": {
              "visible": true,
              "label": "n = 66"
            },
            "mv-size:2": {
              "label": "n = 123"
            }
          },
          "partsOfWhole": {
            "label": true,
            "value": false,
            "percentage": false
          }
        },
        "partsOfWholeBorders": {
          "outer": {
            "color": {
              "hex": "#000000",
              "alpha": 1
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            "thicknessPt": 1
          },
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            "color": {
              "hex": "#000000",
              "alpha": 1
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          }
        }
      },
      "titles": {
        "x": {
          "text": "Rich factor",
          "fontSize": 10
        },
        "y": {
          "text": "-log_{10} P",
          "fontSize": 10
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      }
    }
  ]
}