Shiny apps for pop gen courses.

Created by Silas Tittes and Scott Taylor, for the undergraduate Population Genetics course taught at University of Colorado at Boulder.

This repository consists of multiple sub-directories organized by topic. Each directory has at least one shiny app. Some have multiple.

Dependencies

R and RStudio

Additionally, make sure tidyverse, shiny, and wesanderson packages are installed to ensure all dependencies are available.

#get package names
pckgs <- c("tidyverse", "shiny", "wesanderson")

#determine if packages are installed already
miss <- pckgs[!pckgs %in% installed.packages()]

#install missing packages
if(length(miss)) install.packages(miss, dependencies = TRUE)

How to run apps

To run an app, simply open in RStudio and click the "Run App" button. We prefer to use the "Run External" option (see image), which will open the app in your system's default web browser.

Details

• Drift

  • drift_app.R
    • Two-allele drift-only model. Shows fluctuations in allele frequency over discrete generations. Includes option of imposing a bottleneck (without population size recovery).

• Coalescence

  • discrete_time_app.R
    • Discrete-time forward simulation of sampling alleles. Updated to allow a sample from the population instead of having n = Ne.
  • continuous_coalescence_app.R
    • Create random genealogies and drop mutations along branches (number of mutations recorded in the small box along branches). Option to hide or show the sequence alignment and genealogy (note columns are individuals).

• FST

  • fst_app.R
    • Two deme visualization. Randomly samples alleles according to frequencies specified by user. Prints HS, HT, and FST.

• Selection

  • haploid_selection_app.R
    • Shows change in allele frequency over time due to relative fitness of alleles.
  • diploid_selection_app.R
    • Produces three plot types: average fitness versus allele frequency, change in allele frequency versus allele frequency, and allele frequency over discrete generations.
  • dipoloid_finite_app.R.
    • Traces allele frequencies over discrete generations, where relative fitness of genotypes varies. Like diploid_selection_app.R, but with finite population size. Provides the option to download data, which could be useful for answering questions about fixation probabilities * linked_selection_app.R
    • Compares the effects of background and linked selection on genetic diversity as a function of recombination rate Based on Chapter 9 of Graham Coop's excellent popgen-notes.
  • sweeps_app.R
    • Based on paramter inputs, estimates sojourn time and the size of the region impacted by a selective sweep. I've found this app helpful when trying to come up with expectations for what sweeps will look like under realistic scenerios. Also based on Graham Coop's textbook.

• STRUCTURE

  • structure.R
    • Not a shiny app, Make plots from STUCTURE output.

• Quant-Gen

  • phenotypic_variation.R
  • A really simple demonstration on how additive alleles combined with environmental noise contribute to quantitative traits, and rapidly approximate a normal distribution.

Contribute

I would love to expand and improve these. Please submit pull requests and issues, or email me with suggestions. silas(dot)tittes(at)gmail(dot)com

More resources

Graham Coop's excellent popgen-notes

CJ Battey's DriftR

CJ Battey's AdaptR

CJ Battey's LDsim

Chris Muir's Shiny Apps

Kent Holsinger's Shiny Apps

Liam Revell's Shiny Apps

Sally Otto's Shiny Apps

Acknowledgments

Big thanks for contributions from:

• Liz Scordato
• Tanja Pyhäjärvi
• Yaniv Brandvain
• <Your name here?>