Pantograph Documentation

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Update Data ​

Most data can be extended or updated by admin users of Pantograph:

  • Upload metadata
  • Upload variation tracks
  • Upload expression data

Upload Metadata ​

New or updated metadata should be stored in a comma-separated text file (CSV) and can then be uploaded via the Metadata menu in Pantograph's toolbar.

IMPORTANT

Uploading metadata will replace the currently loaded metadata. To ensure all required information is retained, always include all metadata to be integrated into Pantograph in a single file.

The metadata file must have a header line indicating the metadata categories that will be displayed in Pantograph, and the first column need to be named PathName. Metadata for each track should be listed in a comma-separated list in the same order of metadata categories; see the example metadata file below.

INFO

Both categorical and numerical metadata values are supported and will be automatically identified.

Example Metadata CSV File ​

csv
PathName,cultivation,yield_random  
pathA,cultivated,0.146957  
pathB,landrace,0.326076  
vcfTrack1,cultivated,0.461396  
vcfTrack2,,0.473928

INFO

Missing data is represented by an empty entry in the respective metadata column (e.g., cultivation for vcfTrack2 in the example above).

After the upload, the new data will be available in Pantograph after a reload of the Pantograph website.

Upload Variation Tracks ​

Admin users can upload new variation tracks

To upload new variation tracks, ensure the following requirements are met:

Samplesheet Format:

The samplesheet must be in CSV format (comma-separated).
The header line must follow this format: "group,reference,vcf".

The required samplesheet columns are:

Column 1: Group name for the VCF files (e.g., "vcf_group_1").
Column 2: Name of the reference genome (must match the reference specified in the graph).
Column 3: Path to the VCF file on S3, which can be either:

  • an uncompressed VCF file (.vcf).
  • a bgzip-compressed VCF file (.vcf.gz).

VCF Files on S3:

Place all VCF files listed in the samplesheet into a unique folder on S3. Ensure the file paths specified in Column 3 of the samplesheet correctly point to their respective files in the S3 folder.