MA+Volcano

Last updated: 3 years ago (view history), Time to read: 2 mins

Description

These code block examples can be used to generate MA+Volcano plot by using a BigWig Stranded file as seen in VisCom

Use: The MA plot contrasts the magnitude of expression (M) on the x axis against the amplitude (A) of change between two states. The volcano plot compares the amplitude of change (x-axis ) to the statistical reliability of that change (-log transformed p value, y-axis).

ProteinPaint Google Docs

warning

If you are using DNAnexus links, be sure to extend the duration. See our manage data section. Supported by the Traditional Code Editor only.

URL Parameter EXAMPLE

Be sure to update lines 4, 7, 9, 12, 14 and 17 

{
"genome":"hg19",
"mavolcanoplot": {
    "url": "https://pecan.stjude.cloud/static/pp-support/example.files/DIPG_H33K27MvsWT_noACVR_adj.txt",
    "tracks": [
      {
        "name": "Demo RNA-seq coverage",
        "strand1": {
          "url": "https://westus.dl.azure.dnanex.us/F/D/FqJyV919Y8XGZ0XZ1BFZK53PpzJGqBvV5GKjyx1Z/mavb_demo_sense.bw"
        },
        "strand2": {
          "url": "https://westus.dl.azure.dnanex.us/F/D/FPk82BJpJqp20gZ7Z0ggp1b84XZ8J1KKYx2qz78Z/mavb_demo_sense.bw",
          "normalize": {
            "dividefactor": -1
          }
        },
        "type": "bigwigstranded"
      }
    ]
  }
}
tip

If you are using a path on the HPC, the file must exist in a directory in the /tp directory. For more details, see our manage data section.

Path to file EXAMPLE

Be sure to update lines 4, 7, 9, 12, 14 and 17 

{
"genome":"hg19",
"mavolcanoplot": {
    "url": "https://pecan.stjude.cloud/static/pp-support/example.files/DIPG_H33K27MvsWT_noACVR_adj.txt",
    "tracks": [
      {
        "name": "Demo RNA-seq coverage",
        "strand1": {
          "file": "proteinpaint_demo/hg19/mavb/mavb_demo_sense.bw"
        },
        "strand2": {
          "file": "proteinpaint_demo/hg19/mavb/mavb_demo_antisense.bw",
          "normalize": {
            "dividefactor": -1
          }
        },
        "type": "bigwigstranded"
      }
    ]
  }
}