t-SNE (Sample Scatterplot) - St. Jude Cloud Docs

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.

Warning
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:

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

Select Scatter plot
- Select Example
- Select Code
  - Review the JSON formatting

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/.

Track List and Facet Table

These code block examples can be used to generate Track List and Facet Table as seen in VisCom.

VCF

These code block examples can be used to generate a figure using vcf data as seen in VisCom.