PSY6422_Project

Mini-project focusing on improving visualizations.

Purpose:

The objective of this module project is to recreate a graph from from an undergraduate dissertation titled “The effects of calcium modulators on TDP-43 function and development of a new co-localization protocol in ALS cellular models” using the original data in R, aiming to achieve the following:

1. Develop a visualization that improves upon the aesthetics of the existing graph, enhancing its visual appeal and clarity.
2. Create a visualization that facilitates the interpretation of the obtained data, offering new insight.

Full project is viewable at https://github.com/carlospzhz/PSY6422_Project.

Research Question

The current graph lacks the ability to illustrate the distribution of individual data points. This information is crucial for understanding whether the observed increase in TDP-43 inclusions with MP004 is due to a general augmentation of inclusions across all cells or if it’s primarily driven by a rise in the frequency of cells with significantly higher numbers of inclusions. Thus, recreating the graph aims to answer this question.

This repository contains:

• figures folder which contains:
  1. "Average_number_of_Inclusions_4h" - the original figure.
  2. "NEW_Avg_number_TDP43_inclusions.jpeg" - the final plot produced.
• data folder which contains:
  1. "codebook.txt" - a codebook for interpretation of the variables.
  2. "data_project.xlsx" - raw data used for the analysis and processing.
  3. "processed_data.xlsx" - data processed (long format) in the code used for visualisation.
• index.rmd - RMarkdown file (code)
• index.html - A web page of the markdown file

Installation Instructions

To run this project, you will need the following software and packages:

Dependencies

Software: R (a programming language and environment for statistical computing and graphics) IDE: RStudio (an integrated development environment for R), or other IDE of your liking (check that it’s compatible with R) R Packages: ‘tidyverse’, ‘ggplot2’, ‘gghalves’, ‘see’ Installation steps Install R

1. Download and install R from the CRAN website.

• Follow the installation instructions specific to your operating system.

2. (Optional) Download RStudio Desktop from the RStudio download page.

• Install RStudio by following the provided instructions.
• Install Required Packages

3. Launch R or RStudio and create a new R script (or open the existing markdown file).
4. Copy and paste (or run) the following code found in the "code.R" script to check.

This code can also be found in the markdown file (look for "3.1 Setup and Preparation" and "3.2 Code for Data Visualization" sections). By following these steps, your project environment will be set up with all the necessary software and packages to run the provided R code. This setup will allow you to process the data and generate plots defined in your scripts.

Visualization produced