hidecan

hidecan is an R package that I developed following the publication of my PhD work on the mechanisms of tuber bruising in the tetraploid potato. In this paper, we proposed a new visualisation to present in one single plot results from genome-wide associations studies (GWAS), differential expression (DE) alongside manually curated lists of genes of interest (e.g. candidate genes mined from prior research). We named this new visualisation HIDECAN plots (which stands for HIgh-scoring markers, Differentially Expressed genes and CANdidate genes). The hidecan package follows from this work, by providing a way for users to generate their own HIDECAN plots from their GWAS and DE results. The package offers a suite of functions to easily go from tables of results or of genes of interest to the plot. The package also offers a shiny app that users can use to import their data and generate a plot interactively rather than through code. Lastly, we also offer a helper function to extract necessary information from the results of the GWASpoly package (for GWAS in autotetraploid organisms) into a format that can hidecan accepts. The goal is to facilitate the use of hidecan at the end of an analysis pipeline without having to spend too much time on results formatting.

The package is publicly available on the CRAN and on GitHub, and a preprint is available on BioRxiv. I gave a presentation on hidecan during the 2023 Tools for Polyploids workshop, the recording is available on Youtube.