In Tatianabellagio/buttRflyfish: What the Package Does (One Line, Title Case)

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "README-"
)
# Please put your title here to include it in the file below.
Title <- "buttRflyfish: reproduction of figure 2b from Nowicki et al. 2020"

buttRflyfish

This repository contains the data and code for our package buttRflyfish, which will reproduce figure 2b from Nowicki et al. 2020. The authors analyzed gene expression of socially-relevant neuropeptides across different brain regions in several butterfly fishes. Specifically, they wanted to characterize the neural correlates of pair-bonding versus solitary behavior. Figure 2b shows a significant downregulation of oxytocin receptor in the supracommissural part of the ventral telencephalon in the males of solitary butterfly fish species.

Example

library(buttRflyfish)

data = load_data() # load data
model = run_model(data) # run MCMC model
p = otr_expression_plot(model,data) # plot differential expression results

How to cite

Please cite this compendium as:

Authors, (r format(Sys.Date(), "%Y")). Compendium of R code and data for r Title. Accessed r format(Sys.Date(), "%d %b %Y"). Online at https://github.com/Tatianabellagio/buttRflyfish

Contents

The analysis directory contains:

• :file_folder: paper: R Markdown source document for manuscript. Includes code to reproduce the figures and tables generated by the analysis. It also has a rendered version, paper.docx, suitable for reading (the code is replaced by figures and tables in this file)
• :file_folder: data: Data used in the analysis.

How to run in your browser or download and run locally

This research compendium has been developed using the statistical programming language R. To work with the compendium, you will need installed on your computer the R software itself and optionally RStudio Desktop.

You can download the compendium as a zip from from this URL: master.zip. After unzipping: - open the .Rproj file in RStudio - run devtools::install() to ensure you have the packages this analysis depends on (also listed in the DESCRIPTION file). - finally, open analysis/paper/paper.Rmd and knit to produce the paper.docx, or run rmarkdown::render("analysis/paper/paper.Rmd") in the R console

Licenses

Text and figures : CC-BY-4.0

Code : See the DESCRIPTION file

Data : CC-0 attribution requested in reuse

Contributions

We welcome contributions from everyone. Before you get started, please see our contributor guidelines. Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.

Tatianabellagio/buttRflyfish documentation built on Dec. 18, 2021, 4:05 p.m.