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hidecan is an R package for generating HIDECAN plots, which arevisualisations summarising the results of one or more QTL mapping,genome-wide association study (GWAS) and transcriptomics differentialexpression (DE) analysis, alongside candidate genes of interest.

hidecan is available on the CRAN and can be installed via:

install.packages("hidecan")

Alternatively, you can install the development version ofhidecan fromGitHub with:

# install.packages("devtools")devtools::install_github("PlantandFoodResearch/hidecan")

The hidecan package works as follows:

• it takes as an input one of more data-frames containing QTL mappingresults, GWAS results, differential expression results and list ofcandidate genes of interest;

• it computes the length of each chromosome based on the genomicposition of the regions, markers and genes provided in the input data;

• it filters the datasets to retain significant regions/markers ordifferentially expressed genes, according to a threshold on theirscore and/or log2-fold change. The fold-change is set by the user, andcan be different for QTL mapping, GWAS and differential expressionresults.

• it displays the position of the significant regions, markers and genesalongside candidate genes (HIDECAN plot). The plot can be customisedby the user via a number of parameters (e.g. legend position or labelsize).

The wrapper functionhidecan_plot() performs all of these steps. Itsuse is demonstrated below with an example dataset:

library(hidecan)## Getting an example datasetx<- get_example_data()hidecan_plot(qtl_list=x[["QTL"]],## data-frame of QTL mapping resultsgwas_list=x[["GWAS"]],## data-frame of GWAS resultsde_list=x[["DE"]],## data-frame of DE resultscan_list=x[["CAN"]],## data-frame of candidate genesscore_thr_qtl=-log10(0.0001),## sign. threshold for QTL mappingscore_thr_gwas=-log10(0.0001),## sign. threshold for GWASscore_thr_de=-log10(0.05),## sign. threshold for DElog2fc_thr=0,## log2FC threshold for DElabel_size=2## label size for candidate genes)

If using HIDECAN, please cite:

Angelin-Bonnet, O., Vignes, M., Biggs, P. J., Baldwin, S., & Thomson, S.(2024). Visual Integration of Genome-Wide Association Studies andDifferential Expression Results with the Hidecan R Package. Genes,15(10), 1244.https://doi.org/10.3390/genes15101244