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GenomePaint Profile Gene Value Example

Zhou Lab

Sep 28, 2021

4.5K

The profile gene value (PVG) track is a combination of genomic profiling results and gene-level numerical values over a set of sample. Hover over the bars to reveal more information about the chromatin states. Pair with the chromatin data other types of gene value data, e.g. RNA expression, proteomics, etc. Learn more about the PVG Track.

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runproteinpaint({
  "host": "https://proteinpaint.stjude.org",
  "holder": visualizationContainer[0],
  "parseurl": true,
  "block": true,
  "nobox": 1,
  "noheader": 1,
  "genome": "hg19",
  "nativetracks": "RefGene",
  "position": "chr14:24549316-24584223",
  "tracks": [{
    "type": "profilegenevalue",
    "genevaluetrack": {
      "file": "proteinpaint_demo/hg19/pgv/pgvdemo.fpkm.gz"
    },
    "genevaluetype": "FPKM",
    "legendimg": {
      "file": "proteinpaint_demo/hg19/pgv/HMM.png",
      "width": 400,
      "height": 400
    },
    "name": "Demo chromHMM",
    "genevaluematchname": "sampleID",
    "tracks": [
      {"type": "bedj", "file": "proteinpaint_demo/hg19/pgv/sample1.gz", "stackheight": 18, "stackspace": 1, "toppad": 1, "bottompad": 1, "onerow": 1, "name": "Sample 1", "sampleID": "101"},
      {"type": "bedj", "file": "proteinpaint_demo/hg19/pgv/sample2.gz", "stackheight": 18, "stackspace": 1, "toppad": 1, "bottompad": 1, "onerow": 1, "name": "Sample 2", "sampleID": "102"},
      {"type": "bedj", "file": "proteinpaint_demo/hg19/pgv/sample3.gz", "stackheight": 18, "stackspace": 1, "toppad": 1, "bottompad": 1, "onerow": 1, "name": "Sample 3", "sampleID": "103"},
      {"type": "bedj", "file": "proteinpaint_demo/hg19/pgv/sample4.gz", "stackheight": 18, "stackspace": 1, "toppad": 1, "bottompad": 1, "onerow": 1, "name": "Sample 4", "sampleID": "104"},
      {"type": "bedj", "file": "proteinpaint_demo/hg19/pgv/sample5.gz", "stackheight": 18, "stackspace": 1, "toppad": 1, "bottompad": 1, "onerow": 1, "name": "Sample 5", "sampleID": "105"},
      {"type": "bedj", "file": "proteinpaint_demo/hg19/pgv/sample6.gz", "stackheight": 18, "stackspace": 1, "toppad": 1, "bottompad": 1, "onerow": 1, "name": "Sample 6", "sampleID": "106"}
    ]
  }]
});

Visualization Code

runproteinpaint({
  "host": "https://proteinpaint.stjude.org",
  "holder": visualizationContainer[0],
  "parseurl": true,
  "block": true,
  "nobox": 1,
  "noheader": 1,
  "genome": "hg19",
  "nativetracks": "RefGene",
  "position": "chr14:24549316-24584223",
  "tracks": [{
    "type": "profilegenevalue",
    "genevaluetrack": {
      "file": "proteinpaint_demo/hg19/pgv/pgvdemo.fpkm.gz"
    },
    "genevaluetype": "FPKM",
    "legendimg": {
      "file": "proteinpaint_demo/hg19/pgv/HMM.png",
      "width": 400,
      "height": 400
    },
    "name": "Demo chromHMM",
    "genevaluematchname": "sampleID",
    "tracks": [
      {"type": "bedj", "file": "proteinpaint_demo/hg19/pgv/sample1.gz", "stackheight": 18, "stackspace": 1, "toppad": 1, "bottompad": 1, "onerow": 1, "name": "Sample 1", "sampleID": "101"},
      {"type": "bedj", "file": "proteinpaint_demo/hg19/pgv/sample2.gz", "stackheight": 18, "stackspace": 1, "toppad": 1, "bottompad": 1, "onerow": 1, "name": "Sample 2", "sampleID": "102"},
      {"type": "bedj", "file": "proteinpaint_demo/hg19/pgv/sample3.gz", "stackheight": 18, "stackspace": 1, "toppad": 1, "bottompad": 1, "onerow": 1, "name": "Sample 3", "sampleID": "103"},
      {"type": "bedj", "file": "proteinpaint_demo/hg19/pgv/sample4.gz", "stackheight": 18, "stackspace": 1, "toppad": 1, "bottompad": 1, "onerow": 1, "name": "Sample 4", "sampleID": "104"},
      {"type": "bedj", "file": "proteinpaint_demo/hg19/pgv/sample5.gz", "stackheight": 18, "stackspace": 1, "toppad": 1, "bottompad": 1, "onerow": 1, "name": "Sample 5", "sampleID": "105"},
      {"type": "bedj", "file": "proteinpaint_demo/hg19/pgv/sample6.gz", "stackheight": 18, "stackspace": 1, "toppad": 1, "bottompad": 1, "onerow": 1, "name": "Sample 6", "sampleID": "106"}
    ]
  }]
});

GenomePaint Profile Gene Value Example

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Visualization Code