Genetically modified organisms (GMOs) and cell lines are widely used models in many aspects of biological research. As part of characterising these models, DNA sequencing technology and bioinformatic analyses are used systematically to study their genomes. Large volumes of data are generated and various algorithms are applied to analyse this data, which introduces a challenge with regards to representing all findings in an informative and concise manner. Scientific visualisation can be used to facilitate the explanation of complex genomic editing events such as intergration events, deletions, insertions, etc. However, current visualisation tools tend to focus on numerical data, ignoring the need to visualise editing events on a large yet biologically-relevant scale.
gmoviz is an R package designed to extend traditional bioinformatics
workflows used for genomic characterisation with powerful visualisation
capabilities based on the Circos (Krzywinski et al. 2009) plotting
framework, as implemented in circlize (Gu et al. 2014).
offers the following key features (summarised in the diagram below):
Visualise complex structural variations, particularly relating to tandem insertions
Generate plots in a single function call, or build them piece by piece for finer customisation
Integration with existing Bioconductor data structures
Circos plots have two key components: sectors and tracks. Each sector represents a sequence of interest (such as a chromosome, gene or any other region). Tracks on the other hand are used to display data. For example: