hidecan is an R package for generating HIDECAN plots, which are
visualisations summarising the results of one or more Genome-wide
association study (GWAS) and transcriptomics differential expression
(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 of hidecan from
GitHub 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 GWAS results, differential expression results and list of candidate genes of interest;
-
it computes the length of each chromosome based on the genomic position of the markers and genes provided in the input data;
-
it filters the datasets to retain significant markers or differentially expressed genes, according to a threshold on their score and/or log2-fold change. The fold-change is set by the user, and can be different for GWAS and differential expression results.
-
it displays the position of the significant markers and genes alongside candidate genes (HIDECAN plot). The plot can be customised by the user via a number of parameters (e.g. legend position or label size).
The wrapper function hidecan_plot() performs all of these steps. Its
use is demonstrated below with an example dataset:
library(hidecan)
## Getting an example dataset
x <- get_example_data()
hidecan_plot(
gwas_list = x[["GWAS"]], ## data-frame of GWAS results
de_list = x[["DE"]], ## data-frame of DE results
can_list = x[["CAN"]], ## data-frame of candidate genes
score_thr_gwas = -log10(0.0001), ## sign. threshold for GWAS
score_thr_de = -log10(0.05), ## sign. threshold for DE
log2fc_thr = 0, ## log2FC threshold for DE
label_size = 2 ## label size for candidate genes
)
If using HIDECAN, please cite:
Angelin-Bonnet, O., Vignes, M., Biggs, P. J., Baldwin, S., & Thomson, S. (2023). Visual integration of GWAS and differential expression results with the hidecan R package. bioRxiv, 2023-03. https://doi.org/10.1101/2023.03.30.535015