https://github.com/griffithlab/genvisr-1

This is a read-only mirror of the Bioconductor SVN repository. Package Homepage: http://bioconductor.org/packages/devel/bioc/html/GenVisR.html Bug Reports: https://support.bioconductor.org/p/new/post/?tag_val=GenVisR.
https://github.com/griffithlab/genvisr-1

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This is a read-only mirror of the Bioconductor SVN repository. Package Homepage: http://bioconductor.org/packages/devel/bioc/html/GenVisR.html Bug Reports: https://support.bioconductor.org/p/new/post/?tag_val=GenVisR.

• Host: GitHub
• URL: https://github.com/griffithlab/genvisr-1
• Owner: griffithlab
• License: cc0-1.0
• Created: 2016-02-01T20:54:54.000Z (almost 9 years ago)
• Default Branch: master
• Last Pushed: 2016-01-30T22:20:20.000Z (almost 9 years ago)
• Last Synced: 2024-04-14T06:15:58.326Z (7 months ago)
• Language: R
• Homepage:
• Size: 376 KB
• Stars: 0
• Watchers: 3
• Forks: 3
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# 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

```R

install.packages("devtools")

```

* Install Bioconductor dependencies

```R

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

```R

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

```

* Install GenVisR

```R

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()

[![Coverage Status](https://coveralls.io/repos/griffithlab/GenVisR/badge.svg?branch=master&service=github)](https://coveralls.io/github/griffithlab/GenVisR?branch=master)