README.Rmd

---
title: "seqvisr"
output: github_document
---

[![Build Status](https://app.travis-ci.com/vragh/seqvisr.svg?branch=main)](https://app.travis-ci.com/vragh/seqvisr)

[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.6583981.svg)](https://doi.org/10.5281/zenodo.6583981)

# seqvisr
Biological sequence visualization and auxiliary functions in `R`.

Consists of two main visualization functions: `msavisr()` and `pdomvisr()`.

`msavisr()` takes `FASTA`-formatted multiple sequence alignments (MSAs) as inputs and produces visualizations like the example below:

<!-- <img src="./docs/articles/seqvisr_files/figure-html/msavisr_examples-1.png" alt="msavisr" width="60%" height="60%"/> -->
![msavisr](./docs/articles/seqvisr_files/figure-html/msavisr_examples-1.png){width=60% height=60%}

`pdomvisr()` takes appropriately formatted tabular data and produces domain structure diagrams like the one below:

<!-- <img src="./docs/articles/seqvisr_files/figure-html/annotdat_all-1.png" alt="pdomvisr" width="60%" height="60%"/> -->
![pdomvisr](./docs/articles/seqvisr_files/figure-html/annotdat_all-1.png){width=60% height=60%}

`cdsearchr()` now enables users to submit protein sequence sets to the NCBI CD-SEARCH server and retrieve annotations as a `data.frame` automatically. Example output below:

<!-- <img src="./docs/articles/seqvisr_files/figure-html/cdsearchr_sample_output.png" alt="cdsearchr" width="60%" height="60%"/> -->
![cdsearchr](./docs/articles/seqvisr_files/figure-html/cdsearchr_sample_output.png){width=60% height=60%}

*NEW* as of `v0.2.7`:
`fastodf()` and `fasdirdf()` are two small utility functions that can be used to read in one or more FASTA files into `R` as a `data.frame`. `fastodf()` can be used to read in a single FASTA file, while `fasdirdf()` can be used to read in an entire directory's worth of FASTA files into a single `data.frame`. See `?fastodf` and `?fasdirdf` for examples.

`list_files()` is a wrapper around `base::list.files()` that has been introduced to account for `list.files()` including directory names by default when `recursive = FALSE`. See `?list_files` for clarifications.

## Installation
Ensure that [`devtools`](https://github.com/r-lib/devtools) is installed. Then execute `devtools::install_github("vragh/seqvisr", build_manual = TRUE, build_vignettes = TRUE)` from within `R` to install the package. If the manual and package vignette are not necessary, `build_manual = TRUE, build_vignettes = TRUE` can be omitted.

## Usage
See `?seqvisr`, `?msavisr`, `?pdomvisr`, and `?cdsearchr` (from within `R`) to access documentation and examples for the main functions. Run `browseVignettes("seqvisr")` to access the vignette.

## Citation
Please cite `seqvisr` using [https://doi.org/10.5281/zenodo.6583981](https://doi.org/10.5281/zenodo.6583981).

## License
Released under GPL-3. A copy of the license file can be found in the file `LICENSE` (`LICENCE` is just for `R` purposes).