Lecture 4

4.0 Lesson learning objectives

By the end of this lesson, we should understand what is principal components analysis and how to apply it to our spatial transcriptomic datasets.

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Hands-on component 4

Our in-class hands-on component will involve analyzing either the MERFISH or Visium dataset using principal components analysis to create a data visualization.

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Class Lesson Notes 4

Prof. Fan’s whiteboard notes from class: genomic-data-visualization-classnotes-20220202.pdf (click to download)

Prof. Fan’s code from class: inclass-plotting-20220202.R (click to download)

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Homework Assignment 4

Make a new data visualization of either the MERFISH or Visium dataset using ggplot in R (do not make the same visualizations that were made in class). Write a description of what you did using vocabulary terms from Lesson 1. See slides for more details on what is expected and how to submit your homework.

genomic-data-visualization-HW_1.pptx (click to download)

Make a pull request to submit your homework (due Saturday Midnight).

Please also install the Rtsne package by running in R the command install.packages('Rtsne') for the hands-on component of the next class.