README.Rmd

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# hidecan <img src="man/figures/logo.png" align="right" alt="" width="120" />

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`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.

## Installation

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

```{r, eval = FALSE}
install.packages("hidecan")
```


Alternatively, you can install the development version of `hidecan` from [GitHub](https://github.com/) with:

```{r, eval = FALSE}
# install.packages("devtools")
devtools::install_github("PlantandFoodResearch/hidecan")
```

## Usage

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:

```{r brief-example-hidecan-plot, fig.width = 10, fig.height = 10}
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
)
```

## Citation

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>