Lesson 5: T-distributed Stochastic Neighbor Embedding
Table of ContentsLecture
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
Our in-class hands-on component will analyzing our spatial transcriptomics datasets to create a data visualization using tSNE. We will also use patchwork to create a multipanel plot.
Class Notes
Prof. Fan’s whiteboard notes from class: genomic-data-visualization-Lesson_5.pptx (click to download)
Prof. Fan’s code from class: code-lesson-5.R (click to download)
Homework Assignment
Make a new data visualization of your spatial transcriptomics dataset with a minimum of 2 panels using the dimensionality reduction approaches we have been learning about in class.
Additional details: genomic-data-visualization-HW_3.pptx (click to download)
Use the same process from HW_1 for what is expected and how to submit your homework to the folder hw3/.