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
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All Visualizations

Investigating a Cell Type in MERFISH Dataset

We are given a spatial gene expression dataset with MERFISH technology. We will cluster the cells and try to identify a group of cells to understand their cell type based...

EC Yash Sonthalia

library(tidyverse) merfish=read.csv(‘/Users/yashsonthalia/Documents/JHUCourses/Spring2022/gdv_yash/data/MERFISH_Slice2Replicate2_halfcortex.csv.gz’) rownames(merfish)=merfish$X merfish$X=NULL x_coord=merfish$x y_coord=merfish$y merfish$x=NULL merfish$y=NULL

Identifying Interesting Cells By Spatial Transcriptomics

Expression of 483 genes has been measured in 42519 cells in a segment of brain tissue via MERFISH. Each cell position in the tissue sample has also been recorded. Fluorescence...

Visualization of a Spleen Tissue and is Identification

We are given a spatial protein expression dataset identify its originality. The figures shown above should be labeled A to G from left to right and from top to bottom....

Identifying Splenic Tissue By Spatial Proteomics

Expression of 28 proteins has been measured in 11512 spleen cells by fluorescence intensity. Each cell area and position in the tissue sample has also been recorded. Fluorescence intensity has...

Deciphering the Identity of a Biological Structure Using Proteomics Data

In Figure 1, I chose to visualize quantitative positional data regarding the spatial organization of cells within the proteomics data set. I used the geometric primitive of points to represent...

Analyze the CODEX dataset

I tried to plot the protein expression in clusters and spatial organizations side by side for better comparison. I noticed a large proportion of genes sequenced are immune cell marker...

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 of points to represent single...

Visualization of Spatial Distribution of Mature Oligodendrocyte with Marker Genes

This code tries to find optimal k that clusters the gene so that one cluster has differential expression of marker gene. We need Oligo1, and Oligo2 to be highly expressed,...

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 tSNE. Two populations of cells...