ISAnalytics 1.2.1
In this vignette we offer support for users that wish to use our package outside of RStudio and optionally in remote servers.
To install the package run the following code:
## For release version
if(!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("ISAnalytics")
## For devel version
if(!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("ISAnalytics")To install from GitHub:
# For release version
if (!require(devtools)) {
install.packages("devtools")
}
devtools::install_github("calabrialab/ISAnalytics",
ref = "RELEASE_3_12",
dependencies = TRUE,
build_vignettes = TRUE)
## Safer option for vignette building issue
devtools::install_github("calabrialab/ISAnalytics",
ref = "RELEASE_3_12")
# For devel version
if (!require(devtools)) {
install.packages("devtools")
}
devtools::install_github("calabrialab/ISAnalytics",
ref = "master",
dependencies = TRUE,
build_vignettes = TRUE)
## Safer option for vignette building issue
devtools::install_github("calabrialab/ISAnalytics",
ref = "master")library(ISAnalytics)ISAnalytics has a verbose option that allows some functions to print
additional information to the console while they’re executing.
To disable this feature do:
# DISABLE
options("ISAnalytics.verbose" = FALSE)
# ENABLE
options("ISAnalytics.verbose" = TRUE)
Some functions also produce report in a user-friendly HTML format, to set this feature:
# DISABLE HTML REPORTS
options("ISAnalytics.widgets" = FALSE)
# ENABLE HTML REPORTS
options("ISAnalytics.widgets" = TRUE)We highly encourage the use of widgets because some of the functions included in this package produce extensive and detailed reports that are made easy to explore via HTML format: we are talking, usually, about potentially very large data frames which are highly impractical to print on console.
Since we are aware that not all users can or want to use RStudio, here we present a few proposed solutions to maintain widget functionality.
If code is run on the user machine but from R gui or console, user should not encounter problems, since widgets will be visualized in your preferred browser. If that’s not the case try:
options(browser = "firefox")of course “firefox” can be replaced with whatever is needed.
Users can visualize widgets even if they’re running code on a remote machine via VPN with the use of X11.
Provided the server machine has a browser installed (for example firefox), you can enable X11 via ssh by doing:
ssh YOUR_USERNAME@server_address -X -YOn the client side, users must have an X11 client such as XQuartz to allow X11 forwarding.
If users are working from a Windows machine the procedure is a bit more complicated, since the operating system is not Unix-like.
Once connected, open R and set the browser option, then load ISAnalytics:
options(browser = "firefox")
library(ISAnalytics)The ISAnalytics package (calabrialab, 2021) was made possible thanks to:
This package was developed using biocthis.
R session information.
#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
#> setting value
#> version R version 4.1.0 (2021-05-18)
#> os Ubuntu 20.04.2 LTS
#> system x86_64, linux-gnu
#> ui X11
#> language (EN)
#> collate C
#> ctype en_US.UTF-8
#> tz America/New_York
#> date 2021-06-10
#>
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#>
#> [1] /tmp/RtmpnRhy18/Rinst2bb03b7368fd6d
#> [2] /home/biocbuild/bbs-3.13-bioc/R/libraryThis vignette was generated using BiocStyle (Oleś, 2021) with knitr (Xie, 2021) and rmarkdown (Allaire, Xie, McPherson, Luraschi, et al., 2021) running behind the scenes.
Citations made with knitcitations (Boettiger, 2021).
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[2] C. Boettiger. knitcitations: Citations for ‘Knitr’ Markdown Files. R package version 1.0.12. 2021. <URL: https://CRAN.R-project.org/package=knitcitations>.
[3] G. Csárdi, R. core, H. Wickham, W. Chang, et al. sessioninfo: R Session Information. R package version 1.1.1. 2018. <URL: https://CRAN.R-project.org/package=sessioninfo>.
[4] A. Oleś. BiocStyle: Standard styles for vignettes and other Bioconductor documents. R package version 2.20.0. 2021. <URL: https://github.com/Bioconductor/BiocStyle>.
[5] R Core Team. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing. Vienna, Austria, 2021. <URL: https://www.R-project.org/>.
[6] H. Wickham. “testthat: Get Started with Testing”. In: The R Journal 3 (2011), pp. 5-10. <URL: https://journal.r-project.org/archive/2011-1/RJournal_2011-1_Wickham.pdf>.
[7] Y. Xie. knitr: A General-Purpose Package for Dynamic Report Generation in R. R package version 1.33. 2021. <URL: https://yihui.org/knitr/>.
[8] calabrialab. Analyze gene therapy vector insertion sites data identified from genomics next generation sequencing reads for clonal tracking studies. https://github.com/calabrialab/ISAnalytics - R package version 1.2.1. 2021. DOI: 10.18129/B9.bioc.ISAnalytics. <URL: http://www.bioconductor.org/packages/ISAnalytics>.