Profile Gene Value (PGV)
These code block examples can be used to generate a profile gene value (pvg) as seen in VisCom.
These code block examples can be used to generate a profile gene value (pvg) as seen in VisCom.
Use: Used to display gene. expression results from RNA seq across a cohort of samples.
Warning
If you are using DNAnexus links, be sure to extend the duration. See our manage data section. The file keys can be switched with url keys. Creating a legend is optional.
If you are using DNAnexus links, be sure to extend the duration. See our manage data section. The file keys can be switched with url keys. Creating a legend is optional.
URL Parameter EXAMPLE
Be sure to update line 2, 3, 8, 12, 16. BEDJ keys need to be updated
{
"block": true,
"genome": "hg19",
"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"
}
]
}
]
}