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These pages describe how to interpret and navigate PanViz visualisations. For guidance on how to create new PanViz visualisations readers are directed towards the PanVizGenerator package and its accompanying vignette. PanVizGenerator is part of Bioconductor.
This wiki is accessed when clicking on the question mark in the lower right corner of a PanViz visualisation. For the readers that have arrived here by other means, and do not have a PanViz visualisation at hand, one can be accessed at this repository's webpage (For those on a cellular connection it should be noted that the webpage downloads ~20Mb of data).
PanViz is an interactive HTML-based visualisation of the structure of functionally annotated pangenomes, written using d3.js. The visualisation is not tied to any particular gene clustering tool, though FindMyFriends is particularly well integrated, as it is written by the same person.
The purpose of the visualisation is to allow researchers to investigate how gene functionality is distributed within a pangenome and how the distribution might change as different subsets of the pangenome is selected. The visualisation is divided into four main areas:
The purpose of this part is to allow for selection of subsets of genomes in order to define new pangenomes, as well as selecting single genomes to compare to the current pangenome. Read more...
This area is devoted to the main visualisation. Depending on the state of the visualisation, one of three different visualisations will be present here, either the default circular view, a stacked bar-chart view or a treemap view. Read more...
This part shows a table with all currently selected gene groups along with their classification within the current pangenome. On top a selection of icons specify different means of changing or refining the current selection. Read more...
In the last area different information related to the pangenome, as well as the parts currently below the mouse point, is presented. Read more...
