Spatio-Temporal-Variation of Gene Expression across Different Pathologies Through the Lens of Aging

Below are the R scripts available, along with a step by step explanation of how to compile them.

Prerequisites

• Download the raw tissue data from the gtex database, and leave it in a local directory named "data". File path: \data
• Download the supplementary file "supplementaryfile.xlsx" located in "data" directory as well. It is needed for all scripts that distinguish between AD genes and non-AD genes
• Download "9606.protein.links.v12.0.txt" and store it in the "data" directory

Scripts

auto_normalized.R

This is the first script you should run. Will create "normalized_{tissue name}.txt" and "normalized_{tissue name}.xlsx" for every tissue, in a directory named "output". File path: \output

auto_threshhold.R

Creates a "plot_{tissue name}.png" file for every tissue, in a directory named "plots". File path: \plots

• Uses normalized files produced by auto_normalized.R.
• The plots are # of switching genes x t value

auto_threshhold_ad.R

Creates a "plot_{tissue name}.png" file for every tissue, in a directory named "AD" in the "plots" directory. File path: \plots\AD

• Needs normalized files produced by auto_normalized.R
• Needs "supplementaryfile.xlsx" to be located in the "data" directory
• The plots are # of switching genes x t value, but only for the top 500 AD genes

auto_bargraph.R

Uses normalized files produced by auto_normalized.R. Creates bar graphs "ad_{tissue name}bargraph_t0.5.png" and "all{tissue name}_bargrapht0.5.png" in a directory named "graphs". File path: \graphs

• Needs "supplementaryfile.xlsx" to be located in the "data" directory
• t value can be configured on line 12 of the script to be any number between 0 and 1. The name of the files produced will change accordingly.

auto_sets.R

Creates "{tissue name}_sets.txt" for every tissue in a directory "ad_sets" and "all_sets".

• Needs normalized files produced by auto_normalized.R
• Needs "supplementaryfile.xlsx" to be located in the "data" directory
• Each line of the sets file represents an age group. Line 1 contains switching genes at ages 30-39. Line 2 contains switching genes at ages 40-49, and so on.

Heatmap.R

Creates "heatmap_ad_age.png", "heatmap_ad_life.png", "heatmap_all_age.png", "heatmap_all_life.png" files in the "heatmaps" directory. File path is \heatmaps

• Needs sets files produced by auto_sets.R

connect.R

Creates "heatmap_connectivity.png" and "heatmap_connectivity.xlsx" in the "connectivity" directory. File path is \connectivity

• Needs "9606.protein.links.v12.0.txt" to be located in the "data" directory
• Needs sets files produced by auto_sets.R

Ad_Sets and All_Sets

• Contains a text file for every tissue, containing the switching genes
• ad_sets contains switching alzhiemers genes, all_sets contains all switching genes.
• Each line corresponds to an age group. Some lines may be empty, but there will only be up to five.
  • Line 1: Ages 30-39
  • Line 2: Ages 40-49
  • Line 3: Ages 50-59
  • Line 4: Ages 60-69
  • Line 5: Ages 70-79