README

Yandell R/qtl2shiny project.

• Articles for qtl2shiny
  • Developer Guide
  • Prepare qtl2 data for qtl2shiny
• DEVELOPER.md
• AGENTS.md

What is this repository for?

• Code to create shiny interface for R/qtl2.
• Version 1.1 Guides:
  • R/qtl2shiny Screen Shots
  • R/qtl2shiny User Guide
  • R/qtl2shiny Developer Guide
  • R/qtl2shiny Data Preparation
• Version 1.4 Guides:
  • Shiny Module Organization
  • Workflow with Recla Data

What has been done

• created Shiny interface for R/qtl2 data
  • handles multiple phenotypes and multiple projects
  • creates plots and scans on the fly
  • uses Shiny modules and dashboard
• organized in package R/qtl2shiny
• depends on related packages
  • R/qtl2
  • R/qtl2ggplot2
  • R/qtl2fst
  • R/qtl2pattern
  • R/qtl2mediate
  • R/intermediate

What are open development issues

Major issues

• speed up access
• save intermediate calculations that are reused
• make sure multiple taxa work smoothly

Minor issues

• shiny
  • reveal plots more (settings on sidebar? tabs?)
  • user save settings for quick replay of shiny
• markdown
  • flexdashboard for Rmd to create dynamic reports
  • link Rmd and shiny documents
• genes
  • GeneRegion and GeneExon for multiple traits giving different results
  • upgrade these to use plot_genes
• scans
  • multiple traits now use superset of covariates
  • fixed for Scan1Plot; need to do same for Scan1SNP and possibly elsewhere
• SNP/Gene Action
  • panel appears not to work at all
• reset
  • reset buttons when new dataset (i.e. to Genome Scan)
• winpar
  • get chr:pos from winParApp for user selection
  • better rationalize how this changes when classes change

Contribution guidelines

• Writing tests
• Code review
• Other guidelines

Who do I talk to?

• Brian Yandell
• Karl Broman
  • R/qtl2

Installation

R/qtl2 is now available on CRAN, as are R/qtl2ggplot and R/qtl2pattern.

You first need to install the devtools package, plus a variety of package dependencies. (Additional, secondary dependencies will also be installed). The code below ensures that packages, including devtools, are only installed if they are missing or have been updated on CRAN or GitHub.

# Install `devtools` if not already installed
tryCatch(find.package("devtools"), error = function(e) install.packages("devtools"))
# Install qtl2shiny dependencies from CRAN if not already installed.
devtools::install_cran(c("devtools", "yaml", "jsonlite", "data.table"))
devtools::install_cran(c("RcppEigen", "RSQLite"))
devtools::install_cran(c("tidyverse", "RColorBrewer", "fst", "shiny"))
devtools::install_cran(c("shinydashboard", "grid", "gridBase", "gdata"))
devtools::install_cran(c("GGally", "Rcpp", "mnormt", "corpcor", "plotly"))
# Install other qtl2 packages from CRAN.
devtools::install_cran(c("qtl2", "qtl2fst", "qtl2ggplot", "qtl2pattern"))
# Install byandell packages from GitHub.
devtools::install_github("byandell-sysgen/intermediate")
devtools::install_github("byandell-sysgen/qtl2mediate")
devtools::install_github("byandell-sysgen/qtl2shiny")

To install qtl2shiny with vignettes (takes a bit longer):

devtools::install_github("byandell/qtl2shiny", build_vignettes=TRUE)