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visiumStitched.Rmd
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visiumStitched.Rmd
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---
title: "Introduction to visiumStitched"
author:
- name: Nicholas J. Eagles
affiliation:
- &libd Lieber Institute for Brain Development
email: nickeagles77@gmail.com
- name: Leonardo Collado-Torres
affiliation:
- *libd
- &ccb Center for Computational Biology, Johns Hopkins University
- &jhubiostat Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health
email: lcolladotor@gmail.com
output:
BiocStyle::html_document:
self_contained: yes
toc: true
toc_float: true
toc_depth: 2
code_folding: show
date: "`r doc_date()`"
package: "`r pkg_ver('visiumStitched')`"
vignette: >
%\VignetteIndexEntry{Introduction to visiumStitched}
%\VignetteEngine{knitr::rmarkdown}
%\VignetteEncoding{UTF-8}
---
```{r setup, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
crop = NULL ## Related to https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016656.html
)
```
```{r vignetteSetup, echo=FALSE, message=FALSE, warning = FALSE}
## Track time spent on making the vignette
startTime <- Sys.time()
## Bib setup
library("RefManageR")
## Write bibliography information
bib <- c(
R = citation(),
BiocStyle = citation("BiocStyle")[1],
knitr = citation("knitr")[1],
RefManageR = citation("RefManageR")[1],
rmarkdown = citation("rmarkdown")[1],
sessioninfo = citation("sessioninfo")[1],
testthat = citation("testthat")[1],
visiumStitched = citation("visiumStitched")[1]
)
```
# Basics
## Install `visiumStitched`
`r Biocpkg("visiumStitched")` is a `R` package available from [GitHub](https://github.com/LieberInstitute/visiumStitched).
It can be installed with the following commands in your `R` session:
```{r "install", eval = FALSE}
if (!requireNamespace("remotes", quietly = TRUE)) {
install.packages("remotes")
}
remotes::install("LieberInstitute/visiumStitched")
```
## Other documentation
For now, `r Biocpkg("visiumStitched")` doesn't have a demonstrative vignette as documentation.
Please refer to the [Reference](http://research.libd.org/visiumStitched/reference/index.html) for
info about how to use its functions, and examples.
## Citing `visiumStitched`
We hope that `r Biocpkg("visiumStitched")` will be useful for your research. Please use the following information to cite the package and the overall approach. Thank you!
```{r "citation"}
## Citation info
citation("visiumStitched")
```
# Reproducibility
The `r Biocpkg("visiumStitched")` package `r Citep(bib[["visiumStitched"]])` was made possible thanks to:
* R `r Citep(bib[["R"]])`
* `r Biocpkg("BiocStyle")` `r Citep(bib[["BiocStyle"]])`
* `r CRANpkg("knitr")` `r Citep(bib[["knitr"]])`
* `r CRANpkg("RefManageR")` `r Citep(bib[["RefManageR"]])`
* `r CRANpkg("rmarkdown")` `r Citep(bib[["rmarkdown"]])`
* `r CRANpkg("sessioninfo")` `r Citep(bib[["sessioninfo"]])`
* `r CRANpkg("testthat")` `r Citep(bib[["testthat"]])`
This package was developed using `r BiocStyle::Biocpkg("biocthis")`.
Code for creating the vignette
```{r createVignette, eval=FALSE}
## Create the vignette
library("rmarkdown")
system.time(render("visiumStitched.Rmd", "BiocStyle::html_document"))
## Extract the R code
library("knitr")
knit("visiumStitched.Rmd", tangle = TRUE)
```
Date the vignette was generated.
```{r reproduce1, echo=FALSE}
## Date the vignette was generated
Sys.time()
```
Wallclock time spent generating the vignette.
```{r reproduce2, echo=FALSE}
## Processing time in seconds
totalTime <- diff(c(startTime, Sys.time()))
round(totalTime, digits = 3)
```
`R` session information.
```{r reproduce3, echo=FALSE}
## Session info
library("sessioninfo")
options(width = 120)
session_info()
```
# Bibliography
This vignette was generated using `r Biocpkg("BiocStyle")` `r Citep(bib[["BiocStyle"]])`
with `r CRANpkg("knitr")` `r Citep(bib[["knitr"]])` and `r CRANpkg("rmarkdown")` `r Citep(bib[["rmarkdown"]])` running behind the scenes.
Citations made with `r CRANpkg("RefManageR")` `r Citep(bib[["RefManageR"]])`.
```{r vignetteBiblio, results = "asis", echo = FALSE, warning = FALSE, message = FALSE}
## Print bibliography
PrintBibliography(bib, .opts = list(hyperlink = "to.doc", style = "html"))
```