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
Identifying Mature Oligodendrocytes Using the Canonical Marker Olig1
In Figure 1, I chose to visualize quantitative data regarding the levels of expression of Olig1 (a canonical marker endogenous to mature oligodendrocytes as well as oligodendrocyte precursor cells) across...
identify and visualize the spatial distribution of Mature Oligodendrocytes
My reasoning for why this specific group of cells stands for potentially mature oligodendrocytes:
Homework 3 Yash Sonthalia
*I used some of Dr. Fan’s inclass plotting code as reference on running tSNE
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 has been downsampled to 5000...
Different Ways to Visualize Structure for Visium Data
For all three images, I am visualizing the position of cells in the Visium Dataset, which is quantitative data. In image 1, I am also visualizing the Kmeans clustering grouping...
Identifying Dopaminergic Neurons Using the Expression of Robust Marker Th in a Spatially Resolved Manner
In Figure 1, I chose to visualize quantitative data regarding the levels of expression of Th (a marker whose expression I am using as a proxy for the identification of...
Comparing Galr1 and Galr2 expression frequencies
This visualization compares the Galr1 and Galr2 expression frequencies across different brain areas. The expression frequencies are quantitative, computed by dividing the counts over the total RNA counts per cell....
Spatial distribution of expression of Ptpn4 in Visium dataset
I am visualizing quantitative data of spatial distribution of the expression level of the Ptpn4 gene in the Visium dataset.
