Pantograph Documentation

Appearance

Graph View ​

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

Pantograph Visualization Scheme

Appbar ​

The following pages can be accessed in the appbar on the very top of the page:

Appbar

Project Selection page (button in blue showing the current project name): Switch to other pangenome datasets, if available
Genome View: Switch to Genome View - the overview of graphs within the project
Share and bookmark: Pangenome views can be stored as bookmarks or shared as URLs
Pipeline page: View clustered or exported regions, start and manage pipelines
Help page: opens the Pantograph documentation pages
User account management: Provides change password functionality and logout

Toolbar ​

The toolbar offers these functionalities from left to right:

Toolbar

Dataset: navigate to a chromosome-specific pangenome graph

Bin width: select the zoom level

Tracks menu: (de)select tracks (graph, variant, and BED region tracks) and metadata
Sort Menu: sort graph and variant tracks separately by metadata values or by name, in ascending or descending order
Navigation Menu: navigate to genome-specific coordinates or to genes by name (partial match)
Plot Menu:
  • Interactive PCA plot (if available)
  • Tree Window to browse cluster dendrograms or pre-computed phylogenetic trees
Legend: describes the different colors used for the tracks
Collapse/expand toolbar

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 vcf files anchored to paths in the pangenome
  • BED region tracks: Show provided BED regions along the pangenome (typically QTL regions)

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/updated by admin users.