Lecture 7

7.0 Lesson learning objectives

By the end of this lesson, we should become more comfortable with interpreting our clusters identified from our analysis pipeline thus far using differential gene expression. We will also perform differential expression analysis, learn how to create different data visualizations to summarize our analysis, and use these visualizations and summaries to evaluate our analysis pipeline.

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Hands-on component 7

Our in-class hands-on component will analyzing either the MERFISH or Visium dataset to identify differentially expressed genes and make data visualizations. We will also learn to use gridExtra to make multi-panel plots.

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Class Lesson Notes 7

Prof. Fan’s whiteboard notes from class: genomic-data-visualization-classnotes-20220209.pdf (click to download)

Prof. Fan’s code from class: inclass-plotting-20220209.R (click to download)

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Homework Assignment 7

Make a new multi-panel (at least 2 panels) data visualization of either the MERFISH or Visium dataset using ggplot in R and the concepts we have been learning in class (principal components analysis, tSNE, kmeans clustering, and/or differential gene expression analysis). Write a description of what you did using vocabulary terms from Lesson 1. Refer to slides from Lesson 4 for more details on what is expected and how to submit your homework.

genomic-data-visualization-HW_3.pptx (click to download)

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