10.3.1 Example functionpaste0(date_weekday, ": ", praise::praise())
}weekday_praise()
-#> [1] "Monday: You are exquisite!"
+#> [1] "Tuesday: You are super!"
weekday_praise("2024-06-09")
-#> [1] "Sunday: You are brilliant!"
+#> [1] "Sunday: You are dandy!"
Here’s the full code for the function and its documentation.
#' Praise a weekday#'
diff --git a/dge-model-building-with-variancepartition.html b/dge-model-building-with-variancepartition.html
index 881bbc2..a0fee53 100644
--- a/dge-model-building-with-variancepartition.html
+++ b/dge-model-building-with-variancepartition.html
@@ -314,8 +314,25 @@
## Lets get some data using spatialLIBDsce_layer <- spatialLIBD::fetch_data("sce_layer")#> adding rname 'https://www.dropbox.com/s/bg8xwysh2vnjwvg/Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata?dl=1'
-#> 2024-06-10 23:27:14.700913 loading file /github/home/.cache/R/BiocFileCache/3993f119bd3_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
Sometimes there might be an error, as it might clash with other packages (like plyr). To avoid this, we can use here::here() (which basically clarifies that the requested function is from the here package).
Some useful commands are getwd() and setwd(), which deal with the working directory, which is the default location where R looks for files to read or save.
getwd() retrieves the current working directory.
setwd() allows changing the current working directory.
-
getwd() # returns the current path
-setwd("desired/directory") # changes to the specified path
+
getwd() # returns the current path
+setwd("desired/directory") # changes to the specified path
Best Practice:
Instead of using “setwd” to manually set your working directory, it is often better to use the “here” package. Using “here”
avoids issues with hard-coded paths and ensures your scripts work regardless of the specific setup of your working environment.
-
## Instead of "C:/Users/user/Desktop/data/myfile.csv"
-
-## Use here to construct file paths
-file_path <-here("Users", "user", "Desktop", "data", "myfile.csv")
-# file_path <- here:here("Users", "user", "Desktop","data", "myfile.csv")
-data <-read.csv(file_path)
+
## Instead of "C:/Users/user/Desktop/data/myfile.csv"
+
+## Use here to construct file paths
+file_path <-here("Users", "user", "Desktop", "data", "myfile.csv")
+# file_path <- here:here("Users", "user", "Desktop","data", "myfile.csv")
+data <-read.csv(file_path)
Other examples of how “here” could be used:
-
## Example: save data to a file and load it
-a <-1
-c <-23
-
-save(a, c, file =here("test-data.RData"))
-# save(a, c, file = here:here("test-data.RData"))
-load(here("test-data.RData"))
-# load(here:here("test-data.RData"))
-
-## Create a directory
-dir.create(here("subdirectory"), showWarnings =FALSE)
-# dir.create(here:here("subdirectory"), showWarnings = FALSE)
-
-## Create a file, indicating the subdirectory (the first argument in this case)
-file.create(here("subdirectory", "filename"))
-#> [1] TRUE
## Example: save data to a file and load it
+a <-1
+c <-23
+
+save(a, c, file =here("test-data.RData"))
+# save(a, c, file = here:here("test-data.RData"))
+load(here("test-data.RData"))
+# load(here:here("test-data.RData"))
+
+## Create a directory
+dir.create(here("subdirectory"), showWarnings =FALSE)
+# dir.create(here:here("subdirectory"), showWarnings = FALSE)
+
+## Create a file, indicating the subdirectory (the first argument in this case)
+file.create(here("subdirectory", "filename"))
+#> [1] TRUE
The usethis package simplifies many common setup tasks and workflows in R. It helps streamline the process of creating new projects, setting up Git repositories, and connecting with GitHub. Mastering usethis allows you to focus more on coding and less on configuration.
In this case, the package is already installed so we just need to load it.
✔ indicates that usethis has setup everything for you.
● indicates that you’ll need to do some work yourself.
-
## For example, create a README file
-usethis::use_readme_md()
-#> ✔ Setting active project to '/__w/cshl_rstats_genome_scale_2024/cshl_rstats_genome_scale_2024'
-#> ✔ Writing 'README.md'
+
## For example, create a README file
+usethis::use_readme_md()
+#> ✔ Setting active project to '/__w/cshl_rstats_genome_scale_2024/cshl_rstats_genome_scale_2024'
+#> ✔ Writing 'README.md'
To connect our RStudio repository with GitHub, we request a token, which allows GitHub to grant permission to our computer.
You can request the token using R (choose a meaningful name).
-
## Initiate connection with GitHub
-usethis::create_github_token() # redirects to GitHub where you'll choose a specific name for the token
+
## Initiate connection with GitHub
+usethis::create_github_token() # redirects to GitHub where you'll choose a specific name for the token
Copy the token to enter it later with gitcreds_set()
-
gitcreds::gitcreds_set() # here you place the token (NOT your GitHub password!!!)
+
gitcreds::gitcreds_set() # here you place the token (NOT your GitHub password!!!)
Another way to request the token is by going to GitHub Tokens, this option will provide a recommendation of the parameters to select.
The token expiration parameter can be changed so it does not expire (for security, GitHub does not recommend this). Otherwise, consider its validity period.
@@ -566,27 +583,27 @@
14.3.2 Creating a personal access
You can always generate a new one (don’t forget to delete the previous token).
The next step is to configure our GitHub user in the global .gitconfig file:
-
## Configure GitHub user
-usethis::edit_git_config() # opens the global .gitconfig file
-
-## Place the name and email of your GitHub account.
-## JUST remove the "#" and respect the other spaces
-
-# [user]
-# name = N A M E
-# email = github_email
+
## Configure GitHub user
+usethis::edit_git_config() # opens the global .gitconfig file
+
+## Place the name and email of your GitHub account.
+## JUST remove the "#" and respect the other spaces
+
+# [user]
+# name = N A M E
+# email = github_email
14.3.3 Initialize Git and GitHub repository
Now let’s initialize the repository in Git (locally on your computer) and then request to connect it with GitHub servers. Git is the software while GitHub is the web platform (based on Git) that allows collaboration.
-
## Initialize the Git repository
-usethis::use_git()
-
-## Connect your local Git repository with GitHub servers
-usethis::use_github()
+
## Initialize the Git repository
+usethis::use_git()
+
+## Connect your local Git repository with GitHub servers
+usethis::use_github()
## Write a new file, using here::here to specify the path
-writeLines("hello", here::here("R", "test-here.R"))
-
-## Another way is to use use_r
-usethis::use_r("test-file-github.R") # adds file to the project's R directory
-
-## For example, we might try adding something new
-gert::git_add("R/test-file-github.R")
-
-## Add commit of what was done
-gert::git_commit("uploaded test file")
-
-## Gives info about the commits
-gert::git_log()
-
-## Upload your changes from the local repo to GitHub
-gert::git_push() # IMPORTANT COMMAND
+
## Write a new file, using here::here to specify the path
+writeLines("hello", here::here("R", "test-here.R"))
+
+## Another way is to use use_r
+usethis::use_r("test-file-github.R") # adds file to the project's R directory
+
+## For example, we might try adding something new
+gert::git_add("R/test-file-github.R")
+
+## Add commit of what was done
+gert::git_commit("uploaded test file")
+
+## Gives info about the commits
+gert::git_log()
+
+## Upload your changes from the local repo to GitHub
+gert::git_push() # IMPORTANT COMMAND
It might be more user-friendly to use the Git pane that appears in RStudio :)
@@ -647,7 +664,7 @@
14.4.2 2. Create index.Rmd for th
---
title: "Welcome to My Website"
author: "Your Name"
-date: "2024-06-10"
+date: "2024-06-11"
output: html_document
---
@@ -671,7 +688,7 @@
14.4.2 2. Create index.Rmd for th
14.4.3 3. Render the Site
To render the site, use the rmarkdown::render_site() function, which converts all R Markdown and Markdown files into HTML. The resulting HTML files and resources are placed in a directory, typically _site. RStudio facilitates this process with tools like the “Knit” button for individual pages and the “Build” pane for the entire site.
Common elements, such as shared HTML files and CSS for styling, ensure consistency and avoid redundancy. A well-configured navigation bar enhances user experience by providing easy access to different sections.
## You can install Postcards with the following command:
-# install.packages("postcards")
-
-## Or you can install the latest development version (not recommended):
-# remotes::install_github("seankross/postcards@main")
+
## You can install Postcards with the following command:
+# install.packages("postcards")
+
+## Or you can install the latest development version (not recommended):
+# remotes::install_github("seankross/postcards@main")
14.5.2 Templates
@@ -774,24 +791,24 @@
14.6.1 Create a New Project in RS
An R Markdown document with your site’s content
A sample photo you should replace (with your own)
-
## Create a new project
-usethis::create_project("Your_Username.github.io")
+
## Create a new project
+usethis::create_project("Your_Username.github.io")
14.6.2 Set Up Git and GitHub
To save changes, you need to set up Git and GitHub
-
## Set up Git and GitHub
-usethis::use_git() # Restart the session
-usethis::use_github()
+
## Set up Git and GitHub
+usethis::use_git() # Restart the session
+usethis::use_github()
14.6.3 Choose a Template
-
## Choose only one template (the one you like the most)
-postcards::create_postcard(template ="jolla")
-postcards::create_postcard(template ="jolla-blue")
-postcards::create_postcard(template ="trestles")
-postcards::create_postcard(template ="onofre")
-postcards::create_postcard(template ="solana")
+
## Choose only one template (the one you like the most)
+postcards::create_postcard(template ="jolla")
+postcards::create_postcard(template ="jolla-blue")
+postcards::create_postcard(template ="trestles")
+postcards::create_postcard(template ="onofre")
+postcards::create_postcard(template ="solana")
In this way, you will also get the 2 important files:
An R Markdown document with your site’s content
@@ -809,13 +826,13 @@
14.6.5 Deploy the Page
## Deploy the GitHub page
-rmarkdown::render("index.Rmd")
+
## Deploy the GitHub page
+rmarkdown::render("index.Rmd")
