# :mount_fuji: Fuji plot :mount_fuji:

a circos representation of multiple GWAS results.

## Overview

Fuji plot (a circos representation of multiple GWAS results) was developed to efficiently summarize significant SNPs across dozens of traits ([Kanai, M. _et al_., _Nat. Genet._ 2018](http://dx.doi.org/10.1038/s41588-018-0047-6)). Technically, it is a wrapper script for [Circos](http://circos.ca/), generating input data and configuration files from GWAS results.

<p align="center"><img src="https://mkanai.github.io/assets/img/Kanai2018_Fig1.svg" width="640px"></p>

Fuji plot is named after :mount_fuji: Mt. Fuji in Japan :mount_fuji:, whose ridge and skirts greatly resemble our figure!

<p align="center"><img src="https://i.imgur.com/QXlnKZk.jpg" width="480px"></p>

## Requirements

- [R](https://www.r-project.org/) with [dplyr](https://github.com/tidyverse/dplyr) and [stringr](https://github.com/tidyverse/stringr) packages.
  - To install these packages, type `install.packages("tidyverse")` in R console.
- [Circos](http://circos.ca/)
  - Please follow [their instructions](http://circos.ca/documentation/tutorials/configuration/installation/) to install Circos.
  - For the current version ([v0.69-6](http://circos.ca/distribution/circos-0.69-6.tgz)), you need to apply our [patch](https://gist.github.com/mkanai/be05f40f933112bfb70bb08076cdaa00) to avoid an infinite loop in text arrangements. Alternatively, you can download and use [our patched version](https://www.dropbox.com/s/z6jdwhj0o570fp8/circos-0.69-6-kanai.tgz?dl=0). I will report this issue soon.

## Usage

Please add `circos` to your `PATH` or set `CIRCOS_PATH` in `fujiplot.R` appropriately.

```{sh}
Rscript fujiplot.R input_example/input.txt input_example/traitlist.txt output_example
```

## Inputs

Input files used in [Kanai, M. _et al._ (2018)](http://dx.doi.org/10.1038/s41588-018-0047-6) are provided under `./input_example`.

### Significant trait-associated loci (`input.txt`)

This file provides a concatenated list of all significant _trait-associated_ loci (for each trait). It also defines a unique locus across multiple traits to highlight pleiotropic loci. The required fields are as follows:

- `LOCUS_ID`: Unique ID for each locus
- `CATEGORY`: Trait category
- `TRAIT`: Trait name
- `CHR`: Chromosome
- `BP`: Position (hg19 [default] or hg38 [see below])
- `MARKER`: Marker ID
- `GENE`: Gene symbol

Note: If your input is in hg38, please modify `./config/karyotype.conf` as `karyotype = ./../karyotypes/karyotype.human.hg38.txt`.

### Trait list (`traitlist.txt`)

This file provides a list of traits and their categories. It defines an order of traits and a color of each category in a figure. The required fields are as follows:

- `CATEGORY`: Trait category
- `TRAIT`: Trait name
- `COLOR`: Category color

## Outputs

All output files will be created under `./output`.

### Circos outputs (`circos.{png,svg}`)

This is the raw output from Circos. Unfortunately, we could not figure out the appropriate way to make our [highlights](http://circos.ca/documentation/tutorials/highlights/) (radial lines) over [scatter plots](http://circos.ca/documentation/tutorials/2d_tracks/scatter_plots/). To this end, we edited the svg file using Adobe Illustrator and produced the final figure.

<p align="center"><img src="output_example/circos.svg" width="640px"></p>

### Optional: a bar plot (`barplot.pdf`)

This corresponds to Fig. 1a of [Kanai, M. _et al._ (2018)](http://dx.doi.org/10.1038/s41588-018-0047-6). Again, you need to do some Illustrator edits to make it pretty. You can suppress this output by setting `OUTPUT_BARPLOT = FALSE` in `fujiplot.R`.

## Citation

When using Fuji plot, please cite the following paper.

- Kanai, M., _et al_. Genetic analysis of quantitative traits in the Japanese population links cell types to complex human diseases. _Nat. Genet._ (2018) [doi:10.1038/s41588-018-0047-6](http://dx.doi.org/10.1038/s41588-018-0047-6)

## Contact

Masahiro Kanai (mkanai@g.harvard.edu)

http://mkanai.github.io/

## Links

- [JENGER](http://jenger.riken.jp/en/) (the lab website)
- [The BioBank Japan Project](https://biobankjp.org/english/index.html)
- [RIKEN Center for Integrative Medical Sciences](http://www.ims.riken.jp/english/)
- [National Bioscience Database Center Human Database](https://humandbs.biosciencedbc.jp/en/)
- [Circos](http://circos.ca/)
- [ClicO FS](http://codoncloud.com:3000/)