Welcome
Welcome to the Course Website for EN.580.428 Genomic Data Visualization!
As the primary mode through which analysts and audience members alike consume data, data visualization remains an important hypothesis generating and analytical technique in data-driven research to facilitate new discoveries. However, if done poorly, data visualization can also mislead, bias, and slow down progress. This hands-on course will cover the principles of perception and cognition relevant for data visualization and apply these principles to genomic data, including large-scale single-cell and spatially-resolved omics datasets, using the R statistical programming language. Students will be expected to complete class readings, create weekly data visualizations as homework assignments, and make a major class presentation.
Course Information
Course Staff: Prof. Jean Fan and Lyla Atta
Office Hours: 10:00am-10:50am Monday, Wednesday, and Friday. See Slack for location details.
Lectures: 8:00am-9:50am Monday, Wednesday, and Friday. See Slack for location details.
Course Details
☞ see Course tabFeatured Visualizations
Identifying the Cell-type of a Random Cell Cluster
In Figure 1, I have plotted the spatial distribution of cells within our MERFISH data set, after down-sampling the data. I used the geometric primitive...
Homework 4 Yash Sonthalia
Figure schema as follows: A) Top left B) Top right C) Bottom left D) Bottom right
Mature Oligodendrocytes in MERFISH Data Predicted by high Olig1 expression and low or no Pdgfra expression
Gene expression of 5000 cells was measured by MERFISH. Initially, populations were grouped by the first thirty principle components and visualized in two dimensions by...
Exploration of GFAP expression in Kmeans Clustering of MERFISH data
I am visualizing quantitative data of the expression level after TSNE embedding and kmeans clustering based on that in the MERFISH dataset.
Cells Expressing Gad1 in MERFISH Data Grouped by PCA
My multipanel visualization includes six individual plots. The origin of the data for all plots is the MERFISH dataset (42519 cells x 486 genes) which...
Comparing tSNE and PCA in Visium Data
I am visualizing PC1 and PC2 from PCA in Visium Data as well as tSNE Dimension 1 in Visium. PC1, PC2, and tSNE Dimension 1...
Prevalence of Genes in MERFISH by Order of Magnitude
I am visualizing the genes in the MERFISH dataset proportioned by the number of cells expressing each gene, which is quantitative data.
Spatial Distribution of Microglia, Determined Using CX3CR1 Expression as a Proxy
For homework 1, I chose to visualize quantitative data regarding the levels of expression of CX3CR1 (a marker whose expression I am using as a...
All Visualizations
Spatial Distribution of MERFISH RNA counts
I am visualizing the relationship between the position of cells in the MERFISH dataset (quantitative) and the total RNA counts per cell (quantitative).
Homework 1 Yash Sonthalia
I am making a visualization of the relationship between the spatial location (quantitative) and the expression (quantitative) of Aqp4, a common marker gene for astrocytes in the merfish dataset. The...
Prevalence of Genes in MERFISH by Order of Magnitude
I am visualizing the genes in the MERFISH dataset proportioned by the number of cells expressing each gene, which is quantitative data.
Spatial Distribution of Microglia, Determined Using CX3CR1 Expression as a Proxy
For homework 1, I chose to visualize quantitative data regarding the levels of expression of CX3CR1 (a marker whose expression I am using as a proxy for the identification of...
