index.md

title
Profile Gene Value (PGV)

Description

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.

ProteinPaint Google Docs

!!!warning If you are using DNAnexus links, be sure to extend the duration. See our manage data section. The keys can be switched with keys. Legendimg 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"
                }
            ]
        }
    ]
}