R Programming 101: Setting up R programming environment (R, RStudio and RStudio.cloud)

Key Takeaways

welcome back to the data professor YouTube channel if you are new here my name is tenon Nanta Sanomat and I'm an associate professor of bioinformatics and on this YouTube channel I teach about data science concepts and tutorials so if you're into this kind of content please consider subscribing so in this episode I'm going to cover about how you can go about installing our our studio onto your computer and also how you can also use the cloud-based version called the our studio dot cloud so without further ado let's get started so what you want to do now is to download our into your computer so you want to go to Google type in our project enter and then the first link go to the our - project dot o-r-g and then you want to click on the cran on the Left panel and then you click on one of the links down below which is nearby your own home hey I will click on the cloud version and so depending on which computer you are using you will download the appropriate version so on this computer I'm using currently the windows so I can download the Windows version and if your account a Linux of course go go ahead download the Linux version and if you're on a Mac download the Mac version so if you are on the Linux version there are ways for you to install directly onto your computer via the terminal so let's say you have a Ubuntu and then you want to type in s you do a PT - g ET space install space R - and base again that will allow you to install the our base into your computer ok and then let's say that you have already installed our into your computer so the next part is to acquire the R studio into your computer as well so you want to Google for our studio calm or Google for our studio and then the link will be down below and then you will click on the download link here okay scroll down and to the left it says our studio desktop so you will click on the download link okay and then you click on the appropriate version for your very own computer so it detects automatically that this is a Windows so I can download this by clicking this link here ok but because I already have a our studio on my computer I will not download it so I'll fire up to our studio and this is what it looks like ok so this is the our studio let me maximize the window so the art studio is comprised of the console the terminal which is a tab which you can click to the left ok so you could type in the commands here and to the right on the top you have the environment so when whenever you assign a variable here to the right the environment will also maintain that and let you see which variables you have here I define another variable and so the variable B becomes shown in the environment tab and history will be a history of the commands that I have typed and also there's the connections to be made via the files and database connections and at the bottom part there will be the file location which is the the files and the folders that are on my computer and to the right the tab here will show the plots and graphs enter create it from the our code and packages are the packages that I have installed on my computer the R package so I can simply click on install and then I can type in the name of the package that I would like to install let's say ggplot2 so I type TT block 2 and it will detect that and so you will want to click on the package that you want to install and click on install or alternatively you could also install a package by typing in install packages and then parentheses and then quotation and then the name of the package that you would like to install let's say ggplot2 and now hit enter and then it will start to install so it really detects that luckily I already have ggplot2 installed on my computer so how do I know that if I scroll down here ggplot2 it's already listed or another way is I can just type library ggplot2 and if I could successfully load the library then it means that ggplot2 is already functional online computer in any our project you would like to set your working directory this is one of the very fundamental step that I am recommending anyone to do because sometimes when you you're following along some tutorials and then you discover that when you try to read a file and it doesn't work what happened is because you might be in the wrong folder and so if you're trying to read a text file and your code gives you an error so the error might be due to the fact that you're not in the same working directory as you are supposed to be in so number one make sure that you are in the same folder that you want to be in so let's say that I want to be in the folder called sandbox and currently I'm in here this root directory so if I click here it will show me what is my current working directory which is not the path that I would like to be working in right because I want to be working in the sandbox folder but in reality I am one folder up ok in the root folder of the home so in order to go into the sandbox folder I can click on the sandbox link and you see that the contents of the sandbox appears here and to the top menu bar I would like to click on session click on the set working directory and then to file pane location so this is the file pane and notice here it becomes sandbox okay so it's the same folder that I am in and the folder that I have most of my files here so the code that I have here will generate a dendrogram which will looks kind of like this so it is for one of my research paper and so it is a circular diagram showing the relationship of the low activity peptides and the high activity peptides so this paper has already been accepted for publication in prj eternal so I'll share you the link down below once it becomes available if you're interested in that that's pretty much there is to knowing the our studio interface if you want to run specific lines in the our code here okay you can click on the control enter if you are on a Windows or on a Linux but if you are on a Mac so you want to type in the command + Enter will allow you to run the specific lines and you could do this one by one you know command enter command enter and it'll just scroll down down down down I just press and hold control and hit on the Enter button and it just run line by line and so this code generates the PDFs that you see here okay so generates the PDF files here let's say that you would like to have a file just like this how can you do that you can create a new file you go to file on the menu bar click on new file click on our script and then you type in some of you are coding here and then you click to save you click on file save as and then you type in the name of your code example code dot R what I'd like to do is type r as the capital letter enter and so there you have it example - code R and the file is shown in the file paint location here ok so that's all for using R and R studio and let me show you the our studio cloud you can go to our studio dot cloud and then you want to sign up or you want to log in so logging in is very simple if you have a Google account you can log in with your Google account or you could also log in with your github accounts ok in a few moments it will load ok here he goes so at default it goes to your workspace so to the left you will see that you can create several spaces for your workspace and in each of the workspace you can also have many projects so you could have many space let's say that you have personal projects or you have work project and you could separate that ok let's say that you have some projects for your research thesis you want to put it in a sandbox or you want to name it as your research thesis and you also have projects with your collaborators rename this to be collaborators and then you have many projects shown below and so for this I have the Irish project that I have already created I can click on this X button in order to expand the window so wait a couple of seconds and it should appear ok now it loads here you go this is what it looks like it looks pretty much like in normal our studio on your own Desktop I can type in a 1 signup value of 1 and to the environment you will see one is assigned to a be equals to 2 and I say C equals to a plus B I can run this here and this is what I see so it works like a native our studio and the good thing about this is that you can also share this project ok you have to you have to change the permission to everyone and then you can share the link and then you could type in the email address that you would like to share ok and a song and so in the next episode I'm going to show you how you can create your first our data science project so please stay tuned thank you for watching please like subscribe and share and I'll see you in the next one but in the meantime please check out these videos