Lesson 5: T-distributed Stochastic Neighbor Embedding

Table of Contents

Lecture 5

5.0 Lesson learning objectives

By the end of this lesson, we should understand what is t-distributed stochastic neighbor embedding and how to apply it to our spatial transcriptomic datasets.

Hands-on component 5

Our in-class hands-on component will analyzing either the MERFISH or Visium dataset to create a data visualization using tSNE. We will also critique a data visualization together and do an in-class demonstration of the homework submission process.

Class Lesson Notes 5

Prof. Fan’s whiteboard notes from class: genomic-data-visualization-classnotes-20220204.pdf (click to download)

Prof. Fan’s code from class: inclass-plotting-20220204.R (click to download)

Homework Assignment 5

None. Complete Homework Assignment 4 if you have not done so yet.

Additional resources