Pantograph Documentation

Appearance

Graph View ​

This page displays the pangenome graph of a specific chromosome. It is divided into following parts:

Pantograph Visualization Scheme

Appbar ​

INFO

Clicking on the Pantograph logo opens the genome view

Following pages can be accessed in the appbar on the very top of the page, from left to right:

  • Pipeline page: View clustered or exported regions, start and manage pipelines
  • Share current view: creates a snapshot of the current view. A URL address is generated that can be shared and re-opened in a different webbrowser window for logged in users.
  • Legend: describes the different colors used for the tracks
  • Help page: opens the Pantograph documentation pages

Toolbar ​

Toolbar

The toolbar offers these functionalities from left to right:

  • Dataset: navigate to the chromosome-specific pangenome graphs
  • Bin width: select the zoom level
  • Sort by Metadata: sort the graph tracks and variant tracks separately by the selected metadata values
  • Color by Metadata: colors the tracks by the selected metadata
  • Change sort order
  • Jump menu: opens the jump menu in the sidebar
  • Metadata menu: opens a selection menu in the sidebar to (de)select individual metadata, or to upload new metadata
  • Tracks menu: opens a selection menu in the sidebar to (de)select individual tracks
  • Tree window: opens the tree window to browse cluster dendrograms or pre-computed phylogenetic trees.
  • Layout settings: allows to switch the display of inversions, duplications, and links on or off

Tracks ​

There are three different kind of tracks:

  • Graph tracks: Show the aligned genomic sequences from the pangenome graph
  • Variant tracks: Show variant calls from genotyping analyses anchored to paths in the pangenome
  • QTL tracks: Show provided QTL regions along the pangenome

Metadata ​

Any available meta data associated with each path is displayed as one vertical heatmap per meta data category in front of each row. Meta data can be traits like flowering time, maturity, yield, etc., a haplotype identifier or other categories (e.g. cultivation type, provenance). Categorical as well as quantitative (integer or floating point numbers) are supported and automatically identified.

Tracks can be sorted by metadata categories via the dropdown menu in the toolbar or by clicking small arrows on top of each metadata heatmap. Each repeated click reverts the sort order.

Metadata can be uploaded by admin users.