1 Purpose of this analysis

This notebook illustrates one way that you can use RNA-seq data from refine.bio to perform Uniform Manifold Approximation and Projection (UMAP) and plot the scores using ggplot2.

⬇️ Jump to the analysis code ⬇️

2 How to run this example

For general information about our tutorials and the basic software packages you will need, please see our ‘Getting Started’ section. We recommend taking a look at our Resources for Learning R if you have not written code in R before.

2.1 Obtain the .Rmd file of this analysis

To run this example yourself, download the .Rmd for this analysis by clicking this link.

Clicking this link will most likely send this to your downloads folder on your computer. Move this .Rmd file to where you would like this example and its files to be stored.

You can open this .Rmd file in RStudio and follow the rest of these steps from there. (See our section about getting started with R notebooks if you are unfamiliar with .Rmd files.)

2.2 Set up your analysis folders

Good file organization is helpful for keeping your data analysis project on track! We have set up some code that will automatically set up a folder structure for you. Run this next chunk to set up your folders!

If you have trouble running this chunk, see our introduction to using .Rmds for more resources and explanations.

# Create the data folder if it doesn't exist
if (!dir.exists("data")) {

# Define the file path to the plots directory
plots_dir <- "plots"

# Create the plots folder if it doesn't exist
if (!dir.exists(plots_dir)) {

# Define the file path to the results directory
results_dir <- "results"

# Create the results folder if it doesn't exist
if (!dir.exists(results_dir)) {

In the same place you put this .Rmd file, you should now have three new empty folders called data, plots, and results!

2.3 Obtain the dataset from refine.bio

For general information about downloading data for these examples, see our ‘Getting Started’ section.

Go to this dataset’s page on refine.bio.

Click the “Download Now” button on the right side of this screen.

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