README.md

In byandell/qtl2shiny: Shiny interface for 'qtl2' Fine Mapping

README

Yandell R/qtl2shiny project.

What is this repository for?

• Code to create shiny interface for R/qtl2.
• Version 1.1.2
• See following documents:
  • R/qtl2shiny Screen Shots
  • R/qtl2shiny User Guide
  • R/qtl2shiny Developer Guide
  • R/qtl2shiny Data Preparation

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

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 set of package dependencies: yaml, jsonlite, data.table, and RcppEigen. (Additional, secondary dependencies will also be installed)

install.packages(c("devtools", "yaml", "jsonlite", "data.table", "RcppEigen", "RSQLite"))

You will also need the following packages for qtl2shiny dependencies:

install.packages(c("tidyverse", "RColorBrewer", "fst",
  "shiny", "shinydashboard", "grid", "gridBase", "gdata", "GGally", "Rcpp",
  "mnormt", "corpcor", "qtl2", "qtl2fst", "qtl2ggplot", "qtl2pattern"))

Then, install plotly using devtools::install_github().

library(devtools)
install_github("ropensci/plotly")

Once you have installed these, install qtl2shiny and related packages as

install_github(paste0("byandell/",
  c("intermediate","qtl2mediate","qtl2shiny")))

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

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

byandell/qtl2shiny documentation built on Nov. 9, 2023, 7:58 p.m.