Visualization Community | St. Jude Cloud

ProteinPaint Expression Rank Example

Zhou Lab

Sep 28, 2021

6.5K

RNA Sequencing

The expression rank track shows the ranking of gene expression in each sample, amongst all samples from the same cancer group. Expression rankings are rendered as bar plots under the 0 to 100 scale, 0 for lowest among the group, 100 for highest. Hover over a bar to see the actual rank, FPKM value, along with sample attributes. Learn more about the Expression Rank track.

Loading Visualization

runproteinpaint({
  host: "https://proteinpaint.stjude.org",
  holder: visualizationContainer[0],
  parseurl: true,
  block: true,
  nobox: 1,
  noheader: 1,
  genome: "hg38",
  position: "chr8:127340055-128243343",
  nativetracks: "RefGene",
  tracks: [
    {
      type: "mdsexpressionrank",
      file: "proteinpaint_demo/hg38/exprank/TCGA.fpkm.gz",
      name: "TCGA FPKM demo expression rank",
      sample: "TCGA-GS-A9TQ",
    },
  ]
});

Visualization Code

runproteinpaint({
  host: "https://proteinpaint.stjude.org",
  holder: visualizationContainer[0],
  parseurl: true,
  block: true,
  nobox: 1,
  noheader: 1,
  genome: "hg38",
  position: "chr8:127340055-128243343",
  nativetracks: "RefGene",
  tracks: [
    {
      type: "mdsexpressionrank",
      file: "proteinpaint_demo/hg38/exprank/TCGA.fpkm.gz",
      name: "TCGA FPKM demo expression rank",
      sample: "TCGA-GS-A9TQ",
    },
  ]
});

ProteinPaint Expression Rank Example

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Loading Visualization

Visualization Code