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 Rafael dos Santos Peixoto
Lectures: 8:00am-9:50am Monday, Wednesday, and Friday. See Canvas for location details.
Office Hours: 10:00am-10:50am Monday, Wednesday, and Friday. See Canvas for location details.
Course Details
☞ see Course tabFeatured Visualizations
Locating a cell type in breast tissue using spatial transcriptomics data
Describe your figure briefly so we know what you are depicting (you no longer need to use precise data visualization terms as you have been...
Identifying Cell-type from Breast Cancer Tissue Spatial Transcriptomics Data using K-means Clustering, tSNE, and Wilcox-test
Describe your figure briefly so we know what you are depicting (you no longer need to use precise data visualization terms as you have been...
KRT8 Expression in Breast Cancer
In this visualization, I explore the expression of KRT8, a cancer related gene, in breast cancer tissue. In panel A and E, I use points...
Cell type exploration using differential gene expression analyses
In the above visualization I have identified a cluster that belong to plasma cells or mature B cells. I started with normalizing the gene expression...
The Effects of Normalization & Transformation on Loading Values for PCA
What data types are you visualizing? For the graph titled “Raw Data’s PCA”, I am visualizing the (1) quantitative data of ERBB2 expression, (2) quantitative...
Comparing the effect of tSNE on varying number of PCs:KRT7 expression
I am visualizing the effect of performing non-linear dimensionality reduction (TSNE) on varying number of PCs. The gene expression was normalized (by total gene expression...
Effect of Introducing Principle Components on Non-linear Dimensionality Reduction
What data types are you visualizing? In the multi-panel plot, I am visualizing spatial and quantitative data with diffrerent projection approaches. The visualization contains spatial...
Comparison of Gene Influence on PC1 in Raw and Cell Area-Normalized Data
Write a description describing your data visualization using vocabulary terms from Lesson 1. What data types are you visualizing? What data encodings (geometric primitives and...
Centroid positions, cell and nucleus areas of each cell
What data types are you visualizing? I am visualizing quantitative data of the ratio of nucleus area to cell area for each cell, quantitative data...
CCND1 Expression vs ERBB2 Expression
What data types are you visualizing? I am visualizing quantitative data for the expression counts of ERBB2 and CCND1, as well as the quantitative data...
Spatial Distribution of Gene Expression
What data types are you visualizing? I am visualizing quantitative data of the log-10-transformed expression level of the TP53 gene, quantitative data of the total...
Frequency of Most Expressed Gene in a Spot
What data types are you visualizing? We are visualizing quantitative data, the number of spots in which the gene is most expressed, and categorical data,...
All Visualizations
Identifying Glandular Cells and Adipocytes in Breast Tissue
Describe your figure briefly so we know what you are depicting (you no longer need to use precise data visualization terms as you have been doing). Write a description to...
Visualizing Changes in Clustering from t-SNE Transformation Across Key Principal Component Pairs: Exploring Extremes and Intermediates
What data types are you visualizing? Gene Expression: Quantitative. X,Y positions: Quantitative. Principle Components: Ordinal.
Analysis of most expressed gene (POSTN): PCA, t-SNE, and UMAP Plots
What data types are you visualizing? I am visualizing quantitative data of the most expressed gene POSTN for each cell, and spatial data regarding the x,y positions for each cell...
PCA with Non-normalized and Normalized Data
With this visualization, we are comparing PCA with non-normalized and normalized data. We are encoding the categorical data, spots, using the geometric primitive of point. We encoded the quantitative data,...
Comparison Between Normalized and Non-Normalized Gene Expression Prior to Dimensional Reduction
What question are you exploring? What happens if I do or not not normalize and/or transform the gene expression data (e.g. log and/or scale) prior to dimensionality reduction?
Performing non-linear dimensionality reduction on genes V.S. on PCs
What data types are you visualizing? quantatative data of the percentage of variance explained by each principal component; quantatative data of CD74 gene expression; quantatative data of pc1 and pc2...
Comparison of non-normalized and log-normalized gene expression data with Principal Component Analysis
Description of data visualization In this data visualization, I have plotted four graphs. The primary aim of the visualization is to compare between gene expression data that has not been...
The Effects of Normalization & Transformation on Loading Values for PCA
What data types are you visualizing? For the graph titled “Raw Data’s PCA”, I am visualizing the (1) quantitative data of ERBB2 expression, (2) quantitative data of CPB1 expression, (3)...
Performance of Nonlinear Dimensionality Reduction on Genes and PCA
Write a description of your data visualization
The Impact of Normalization on Dimensionality Reduction: IGKC Expression Level Case Study
What data types are you visualizing? IGKC gene expression count: quantatative PC 1 and 2 scores: quantatative t-SNE coordinates emb1 and emb2: spatial
Linear vs Nonlinear Dimensionality Reduction on Eevee Dataset
What’s the difference if I perform linear or nonlinear dimensionality reduction to visualize my cells in 2D? There are fundamental differences in performing Principal Component Analysis (PCA), or a linear...
