Yandell R/qtl2shiny project.
- Code to create shiny interface for R/qtl2.
- Version 1.1.2
- See following documents:
- 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
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
- Writing tests
- Code review
- Other guidelines
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)