t-SNE (Sample Scatterplot)

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

Description

These code block examples can be used to generate a t-SNE as seen in VisCom.

Use: tSNE plots are a display that converts high dimensional data to an interpretable proximity plot such that similarity may be assessed across RNA-seq profiles. ProteinPaint Google Docs

URL Key Example

This currently is not supported with a url key at this time.

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.

File key Example

Be sure to update lines 8, 9, 14, 15

{
	"genome": "hg38",
	"mdssamplescatterplot": {
        "mds": {
            "dslabel": "Pediatric2",
            "querykey": "svcnv"
        },
        "analysisdata_file": "proteinpaint_demo/hg38/mdstsne/file.json",
        "dimensions": {
            "width": 700,
            "height": 400
        }
    }
}

If you need an example of how the JSON should be formatted, you can:

  1. Example 1: Go to https://proteinpaint.stjude.org/

    • Select Scatterplot

      • Select Example

      • Select Code

        • Review the JSON formatting
  2. Go here to see a VisCom example.

Furthermore, you can have your excel sheet converted to JSON; there are many ways to do this, but one example is using BeautifyTools and debug by using https://jsonlint.com/.