From c031713c07f138916c3bb4e8a0980e44332d2d16 Mon Sep 17 00:00:00 2001
From: Carine Rey <carine.rey@ens-lyon.fr>
Date: Tue, 6 Sep 2022 17:24:41 +0200
Subject: [PATCH] put bioincoductor/github installing tuto in the main file
(session1)
---
session_1/bioconductor.Rmd | 41 -------------------------------
session_1/github.Rmd | 50 --------------------------------------
session_1/session_1.Rmd | 48 +++++++++++++++++++++++++++++++++++-
3 files changed, 47 insertions(+), 92 deletions(-)
delete mode 100644 session_1/bioconductor.Rmd
delete mode 100644 session_1/github.Rmd
diff --git a/session_1/bioconductor.Rmd b/session_1/bioconductor.Rmd
deleted file mode 100644
index a207936..0000000
--- a/session_1/bioconductor.Rmd
+++ /dev/null
@@ -1,41 +0,0 @@
----
-title: 'R.1: Installing packages from Bioconductor'
-author: "Carine Rey [carine.rey@ens-lyon.fr](mailto:carine.rey@ens-lyon.fr), Laurent Modolo [laurent.modolo@ens-lyon.fr](mailto:laurent.modolo@ens-lyon.fr)"
-date: "2021"
-output:
- rmdformats::downcute:
- self_contain: true
- use_bookdown: true
- default_style: "dark"
- lightbox: true
- css: "../src/style.css"
----
-
-```{r setup, include=FALSE}
-rm(list=ls())
-knitr::opts_chunk$set(echo = TRUE)
-knitr::opts_chunk$set(comment = NA)
-```
-```{r klippy, echo=FALSE, include=TRUE}
-klippy::klippy(
- position = c('top', 'right'),
- color = "white",
- tooltip_message = 'Click to copy',
- tooltip_success = 'Copied !')
-```
-
-To install packages from [bioconductor](http://www.bioconductor.org) you must first install a package called "BiocManager".
-This package imports a function called "install" allowing you to install packages hosted in bioconductor from their name.
-
-To install "BiocManager" you must type:
-
-```R
-install.packages("BiocManager")
-```
-
-Then to install, for example "tximport", you just have to write:
-
-```R
-BiocManager::install("tximport")
-```
-
diff --git a/session_1/github.Rmd b/session_1/github.Rmd
deleted file mode 100644
index 4df196a..0000000
--- a/session_1/github.Rmd
+++ /dev/null
@@ -1,50 +0,0 @@
----
-title: 'R.1: Installing packages from github'
-author: "Carine Rey [carine.rey@ens-lyon.fr](mailto:carine.rey@ens-lyon.fr), Laurent Modolo [laurent.modolo@ens-lyon.fr](mailto:laurent.modolo@ens-lyon.fr)"
-date: "2021"
-output:
- rmdformats::downcute:
- self_contain: true
- use_bookdown: true
- default_style: "dark"
- lightbox: true
- css: "../src/style.css"
----
-
-```{r setup, include=FALSE}
-rm(list=ls())
-knitr::opts_chunk$set(echo = TRUE)
-knitr::opts_chunk$set(comment = NA)
-```
-```{r klippy, echo=FALSE, include=TRUE}
-klippy::klippy(
- position = c('top', 'right'),
- color = "white",
- tooltip_message = 'Click to copy',
- tooltip_success = 'Copied !')
-```
-
-If you need to install a package that is not available on the CRAN but on a github repository, you can do it using the "remotes" package. Indeed this package imports functions that will allow you to install a package available on [github](https://github.com/) or bitbucket or gitlab directly on your computer.
-
-To use the "remotes" packages, you must first install it:
-
-```R
-install.packages("remotes")
-```
-
-Once "remotes" is installed, you will be able to install all R package from github or from their URL.
-
-For example, if you want to install the last version of a "gganimate", which allow you to animate ggplot2 graphes, you can use :
-
-```R
-remotes::install_github("thomasp85/gganimate")
-```
-
-By default the latest version of the package is installed, if you want a given version you can specify it :
-
-```R
-remotes::install_github("thomasp85/gganimate@v1.0.7")
-```
-
-You can find more information in the documentation of remotes : [https://remotes.r-lib.org](https://remotes.r-lib.org)
-
diff --git a/session_1/session_1.Rmd b/session_1/session_1.Rmd
index 662dd28..0ca151f 100644
--- a/session_1/session_1.Rmd
+++ b/session_1/session_1.Rmd
@@ -84,7 +84,7 @@ Reasons to use it:
- It has a large (and growing) user base among scientists
- It has a large library of external packages available for performing diverse tasks.
-```{r echo=F}
+```{r echo=F, message=F}
cran_packages <- nrow(available.packages(repos = "http://cran.us.r-project.org"))
if (! require("rvest")) {
@@ -491,6 +491,7 @@ Instead we are going to use the Rstudio code editor panel, to write our code.
You can go to **File > New File > R script** to open your editor panel.
+
## Writing function
We can define our own function with :
@@ -719,6 +720,8 @@ To install packages from [Bioconducor](http://www.bioconductor.org) and [github]
## Installing packages
+### From CRAN
+
To install packages, you can use the `install.packages` function (don't forget to use tabulation for long variable names).
```R
@@ -740,6 +743,49 @@ install.packages("ggplot2")
</p>
</details>
+### From Bioconducor
+
+To install packages from [bioconductor](http://www.bioconductor.org) you must first install a package called "BiocManager".
+This package imports a function called "install" allowing you to install packages hosted in bioconductor from their name.
+
+To install "BiocManager" you must type:
+
+```R
+install.packages("BiocManager")
+```
+
+Then to install, for example "tximport", you just have to write:
+
+```R
+BiocManager::install("tximport")
+```
+
+### From github
+
+If you need to install a package that is not available on the CRAN but on a github repository, you can do it using the "remotes" package. Indeed this package imports functions that will allow you to install a package available on [github](https://github.com/) or bitbucket or gitlab directly on your computer.
+
+To use the "remotes" packages, you must first install it:
+
+```R
+install.packages("remotes")
+```
+
+Once "remotes" is installed, you will be able to install all R package from github or from their URL.
+
+For example, if you want to install the last version of a "gganimate", which allow you to animate ggplot2 graphes, you can use :
+
+```R
+remotes::install_github("thomasp85/gganimate")
+```
+
+By default the latest version of the package is installed, if you want a given version you can specify it :
+
+```R
+remotes::install_github("thomasp85/gganimate@v1.0.7")
+```
+
+You can find more information in the documentation of remotes : [https://remotes.r-lib.org](https://remotes.r-lib.org)
+
## Loading packages
Once a package is installed, you need to load it in your R session to be able to use it.
--
GitLab