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Fix spaces and add images
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@Melii99
Melii99 committed Jun 5, 2024
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87 changes: 22 additions & 65 deletions 24_postcards.Rmd
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Expand Up @@ -25,21 +25,17 @@ The base directory it takes will be the one you are in when you load the here pa
In this case, the package is already installed so we just need to load it.

```{r, eval=FALSE, warning=FALSE, message=FALSE}
## Install the package manually
# install.packages("here")
## Load "here" (previously installed)
library("here")
```

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).

```{r, here::here, eval=FALSE, warning=FALSE, message=FALSE}
here::here()
```

Some usefull 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.
Expand All @@ -49,33 +45,29 @@ Some usefull commands are "getwd" and "setwd", which deal with the working direc
- setwd() allows changing the current working directory.

```{r, check_paths, eval=FALSE, warning=FALSE, message=FALSE}
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.
```{r, bestpractice, eval=FALSE, warning=FALSE, message=FALSE}

```{r, bestpractice, eval=FALSE, warning=FALSE, message=FALSE}
## 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:

```{r, here_examples, eval=FALSE, warning=FALSE, message=FALSE}
## Example: save data to a file and load it
a <- 1
c <- 23
Expand All @@ -100,7 +92,6 @@ file.show(here("subdirectory", "filename"))
## For example, if we want to see our files in the directory
list.files(here(), recursive = TRUE)
# list.files(here:here(), recursive = TRUE)
```


Expand All @@ -111,38 +102,32 @@ The usethis package simplifies many common setup tasks and workflows in R. It he
In this case, the package is already installed so we just need to load it.

```{r, load_usethis, eval=FALSE, warning=FALSE, message=FALSE}
## Install the package manually
# install.packages("usethis")
## Load "usethis (previously installed)
library("usethis")
```

Usage:

All use_* functions operate on the current directory.

```{r, use_*, eval=FALSE, warning=FALSE, message=FALSE}
# usethis::use_*()
## usethis::use_*()
usethis::use_r()
usethis::use_git()
usethis::use_readme_md()
```

✔ indicates that usethis has setup everything for you.
● indicates that you'll need to do some work yourself.

```{r, usethis_example, eval=FALSE, warning=FALSE, message=FALSE}
## For example, create a README file
usethis::use_readme_md()
#> ✔ Writing 'README.md'
#> ● Edit 'README.md'
```

More functions in usethis:
Expand All @@ -153,14 +138,14 @@ In the following exercises, we will see some uses of usethis.

## Git + GitHub

[GitHub](https://github.com/)

[An Intro to Git and GitHub for Beginners (Tutorial) by HubSpot](https://product.hubspot.com/blog/git-and-github-tutorial-for-beginners)

Version control is a critical skill. Git helps you track changes in your projects, collaborate with others, and maintain a history of your work.

GitHub, a platform for hosting Git repositories, enables seamless collaboration and sharing of your projects with the world. Understanding Git and GitHub ensures your projects are well-organized and accessible.

[GitHub](https://github.com/)

### Prerequisites

We need a GitHub account. If you don't have one, now is the time to create it!
Expand All @@ -173,18 +158,16 @@ We also need to install Git on our computers as the "gitcreds" package requires

After installing Git, restart RStudio to allow it to annex.

```{r, install_gitreq, eval=FALSE, warning=FALSE, message=FALSE}
# Hay que agregarlos a los paquetes a instalar !!!
***Hay que agregarlos a los paquetes a instalar ??? ***

```{r, install_gitreq, eval=FALSE, warning=FALSE, message=FALSE}
## Packages we will need
install.packages(c("gitcreds", "gert", "gh"))
## Load them separately
library("gitcreds")
library("gert")
library("gh")
```

### Creating a personal access token (PAT)
Expand All @@ -194,18 +177,14 @@ To connect our RStudio repository with GitHub, we request a token, which allows
You can request the token using R (choose a meaningful name).

```{r, token, eval=FALSE, warning=FALSE, message=FALSE}
## 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()

```{r, gitcreds, eval=FALSE, warning=FALSE, message=FALSE}
gitcreds::gitcreds_set() # here you place the token (NOT your GitHub password!!!)
```

Another way to request the token is by going to [GitHub Tokens](https://github.com/settings/tokens), this option will provide a recommendation of the parameters to select.
Expand All @@ -220,7 +199,6 @@ Another way to request the token is by going to [GitHub Tokens](https://github.c
The next step is to configure our GitHub user in the .gitconfig file:

```{r, git_config, eval=FALSE, warning=FALSE, message=FALSE}
## Configure GitHub user
usethis::edit_git_config() # opens the .gitconfig file
Expand All @@ -230,21 +208,18 @@ usethis::edit_git_config() # opens the .gitconfig file
# [user]
# name = N A M E
# email = github_email
```

### 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).

```{r, git_repo, eval=FALSE, warning=FALSE, message=FALSE}
## Initialize the Git repository
usethis::use_git()
## Connect your local Git repository with GitHub servers
usethis::use_github()
```

** Done **
Expand All @@ -253,9 +228,7 @@ usethis::use_github()
Useful command to check configuration:

```{r, gh_whoami, eval=FALSE, warning=FALSE, message=FALSE}
gh::gh_whoami()
```


Expand All @@ -270,7 +243,6 @@ Some useful commands for this are:
- git_push

```{r, git_commands, eval=FALSE, warning=FALSE, message=FALSE}
## Write a new file, using here::here to specify the path
writeLines("hello", here::here("R", "test-here.R"))
Expand All @@ -288,13 +260,11 @@ 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 :)

** Agregar imagen del panel !!! **

![](https://raw.githubusercontent.com/lcolladotor/cshl_rstats_genome_scale_2024/devel/Figures/Git_Rstudio.png)

## R websites

Expand All @@ -307,7 +277,6 @@ Creating a website with R Markdown involves several key steps. First, you set up
YAML (.yml file)

```
name: "My Website"
output_dir: "docs"
navbar:
Expand All @@ -321,18 +290,16 @@ output:
html_document:
theme: cosmo
highlight: tango
```

### 2. Create index.Rmd for the Homepage

The homepage is created using an index.Rmd file, which acts as the main entry point for visitors, providing an introduction or overview of the site. Additional pages, such as about.Rmd, offer more detailed information about the website or its author.


Markdown (.Rmd file)
Markdown (index.Rmd file)

```
---
title: "Welcome to My Website"
author: "Your Name"
Expand All @@ -355,7 +322,6 @@ Here is an example of a simple analysis:
summary(cars)
# ```
```

### 3. Render the Site
Expand All @@ -365,9 +331,7 @@ To render the site, use the rmarkdown::render_site() function, which converts al
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.

```{r, render_site, eval=FALSE, warning=FALSE, message=FALSE}
rmarkdown::render_site()
```

### 4. Publish the Website
Expand Down Expand Up @@ -395,9 +359,12 @@ On Netlify, configure the deployment settings to specify the build command (rmar

The postcards package makes it easy to create beautiful, single-page websites with minimal effort. It's perfect for personal websites, portfolios, and project showcases. Using postcards allows you to present your work professionally and creatively, without needing extensive web development knowledge.

>
> ***A collection of R Markdown templates for creating simple and easy-to-personalize single-page websites.***
>
> "The goal of the package is to make it easy for anyone to create a one-page personal website using an R Markdown document."
>

- Author: Sean Kross [aut, cre]

Expand Down Expand Up @@ -429,38 +396,36 @@ In this case, the package is already installed
Agregar postcards a los paquetes !!!!

```{r, install_postcards, eval=FALSE, warning=FALSE, message=FALSE}
## 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")
```

### Templates

Postcards include five templates: Jolla, Jolla Blue, Trestles, Onofre, and Solana. Each site is optimized for viewing on both desktop and mobile devices. The goal of the package is to make it easy for anyone to create a one-page personal website using an R Markdown document.

#### Jolla:
- Jolla:

![Jolla](https://raw.githubusercontent.com/Melii99/rnaseq_2024_postcards/master/Templates/jolla_preview.png)
![](https://raw.githubusercontent.com/Melii99/rnaseq_2024_postcards/master/Templates/jolla_preview.png)

#### Jolla Blue:
- Jolla Blue:

![Jolla Blue](https://raw.githubusercontent.com/Melii99/rnaseq_2024_postcards/master/Templates/jolla_blue_preview.png)
![](https://raw.githubusercontent.com/Melii99/rnaseq_2024_postcards/master/Templates/jolla_blue_preview.png)

#### Trestles:
- Trestles:

![Trestles](https://raw.githubusercontent.com/Melii99/rnaseq_2024_postcards/master/Templates/trestles-preview.png)
![](https://raw.githubusercontent.com/Melii99/rnaseq_2024_postcards/master/Templates/trestles-preview.png)

#### Onofre:
- Onofre:

![Onofre](https://raw.githubusercontent.com/Melii99/rnaseq_2024_postcards/master/Templates/onofre-preview.png)
![](https://raw.githubusercontent.com/Melii99/rnaseq_2024_postcards/master/Templates/onofre-preview.png)

#### Solana:
- Solana:

![Solana](https://raw.githubusercontent.com/Melii99/rnaseq_2024_postcards/master/Templates/solana-preview.png)
![](https://raw.githubusercontent.com/Melii99/rnaseq_2024_postcards/master/Templates/solana-preview.png)

To start personalizing one of these templates, you need to create a new project.

Expand Down Expand Up @@ -493,35 +458,29 @@ Select "Create Project" after choosing a name for the folder that will contain y
- A sample photo you should replace (with your own)

```{r, postcards_project, eval=FALSE, warning=FALSE, message=FALSE}
## Create a new project
usethis::create_project("Your_Username.github.io")
```

### Set Up Git and GitHub

To save changes, you need to set up Git and GitHub

```{r, setup_gitpcds, eval=FALSE, warning=FALSE, message=FALSE}
## Set up Git and GitHub
usethis::use_git() # Restart the session
usethis::use_github()
```

### Choose a Template

```{r, choose_template, eval=FALSE, warning=FALSE, message=FALSE}
## 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:
Expand All @@ -545,10 +504,8 @@ In RStudio, you can use the "Knit" button
or directly:

```{r, deploy_postcards, eval=FALSE, warning=FALSE, message=FALSE}
## Deploy the GitHub page
rmarkdown::render("index.Rmd")
```

** Done **
Expand Down

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