hiuyu / genvisr

Genome data visualizations

GenVisR

Intuitively visualizing and interpreting data from high-throughput genomic technologies continues to be challenging. GenVisr (Genomic Visualizations in R) attempts to alleviate this burden by providing highly customizable publication-quality graphics focused primarily on a cohort level (i.e., multiple samples/patients). GenVisr attempts to maintain a high degree of flexibility while leveraging the abilities of ggplot2 and bioconductor to achieve this goal.

Installation Instructions

Note requires R >= 3.2.1, see Description file for a full list of dependencies

• Install devtools

install.packages("devtools")

• Install Bioconductor dependencies

source("http://bioconductor.org/biocLite.R")
biocLite(c("AnnotationDbi", "biomaRt", "Biostrings", "GenomicFeatures", "GenomicRanges", "Rsamtools"))

• It is suggested but not required to install knitr and rmarkdown for vignette creation

install.packages(c("rmarkdown", "knitr"))

• Install GenVisR

devtools::install_github("griffithlab/GenVisR")

Tips for developers

• It is recommended to use Rstudio for development, Clone the repo and open the "GGgenome.Rproj" folder in Rstudio.
• It is necessary to manual install all packages (since you are cloning and building, not installing), all packages within the imports, Depends, and Suggests flags in the "DESCRIPTION" file (~/GenVisR/DESCRIPTION) should be installed! The r-package devtools should be installed as well!
• Build and Reload the package at this step (shorcut: Shift+Cmd+B)
• GenVisR uses roxygen2 for documentation, to update the Reference Manuscript edit the roxygen2 flags (i.e. @param, @details, etc.) in the code. These are within the R function files in ~/GenVisR/R/, Then run devtools::document().
• To update the vignette edit the R markdown file in the vignettes subdirectory (~/GenVisR/vignettes/GenVisR_intro.Rmd) and press the knit button in Rstudio
• Code for GenVisR is within the R subdirectory (~/GenVisR/R/), make changes there. Be sure to build and reload the package from Rstudio to test changes (Rstudio -> Build -> Build & Reload || Shift+CMD+B)
• test cases are in the test subdirectory (~/GenVisR/tests/testthat/), tests must be named with the character string "test" in the beginning of the name (i.e. for the waterfall function the test file would look like test-waterfall.R). To run tests run devtools::test()