updated scripts

smenon2 · smenon2 · commit d917a68a9aaf · 2026-02-05T13:50:11.000-08:00
diff --git a/QC_CelltypeAnnotation/001_Fig1_Sex_Age.R b/QC_CelltypeAnnotation/001_Fig1_Sex_Age.R
@@ -1,3 +1,5 @@
+# Plotting QC statistics -- specificially about sex and age of the cohort
+# Updated Jan 2026
 
 setwd("/gladstone/corces/lab/users/smenon/2304_PDMultiome_Final/Final_Objects/Scripts/Figure_Plotting/")
 source("plotting_helper_corces.R")
diff --git a/QC_CelltypeAnnotation/002_Fig1_UMAPs.R b/QC_CelltypeAnnotation/002_Fig1_UMAPs.R
@@ -1,3 +1,6 @@
+# Script to plot UMAPs
+# Updated Jan 2026
+
 library(ggrastr)
 library(BuenColors)
 library(ArchR)
diff --git a/QC_CelltypeAnnotation/003_Fig1_QC.R b/QC_CelltypeAnnotation/003_Fig1_QC.R
@@ -1,3 +1,6 @@
+# Plots single cell QC statistics
+# Updated Jan 2026
+
 library(ArchR)
 library(Seurat)
 
diff --git a/QC_CelltypeAnnotation/004_Fig2_RegionHeatmap.R b/QC_CelltypeAnnotation/004_Fig2_RegionHeatmap.R
@@ -1,3 +1,6 @@
+# Script to plot region based subclustering results
+# Updated Jan 2026
+
 library(data.table)
 
 # list all directories that start with "task_"
diff --git a/QC_CelltypeAnnotation/005_Fig1_markerGeneHeatmap.R b/QC_CelltypeAnnotation/005_Fig1_markerGeneHeatmap.R
@@ -1,3 +1,6 @@
+# Script for marker gene heatmap for Figure 1
+# Updated Jan 2026
+
 library(tidyverse)
 library(pheatmap)
 library(scales)
diff --git a/QC_CelltypeAnnotation/007_Fig2_OligoModules.R b/QC_CelltypeAnnotation/007_Fig2_OligoModules.R
@@ -1,4 +1,5 @@
-
+# Script for oligodendrocyte modules
+# Updated Jan 2026
 library(hdWGCNA)
 library(enrichR)
 
diff --git a/QC_CelltypeAnnotation/008_Fig1_CellTypeComposition.R b/QC_CelltypeAnnotation/008_Fig1_CellTypeComposition.R
@@ -1,3 +1,6 @@
+# Script for analyzing cell type composition 
+# Updated Jan 2026
+
 library(ggrastr)
 library(BuenColors)
 library(ArchR)
diff --git a/QC_CelltypeAnnotation/009_Fig1_DopaSubcluster.R b/QC_CelltypeAnnotation/009_Fig1_DopaSubcluster.R
@@ -1,3 +1,6 @@
+# script for dopaminergic neuron subclustering
+# Updated Jan 2026
+
 library(ggrastr)
 library(BuenColors)
 library(ArchR)
diff --git a/QC_CelltypeAnnotation/010_Fig1_RegionalSubclustering.R b/QC_CelltypeAnnotation/010_Fig1_RegionalSubclustering.R
@@ -1,3 +1,6 @@
+# Script for regional subclustering across cell types
+# Updated Jan 2026
+
 library(ggrastr)
 library(BuenColors)
 library(ArchR)
diff --git a/QTLs/001_rasqual_process.R b/QTLs/001_rasqual_process.R
@@ -1,3 +1,6 @@
+# Script used to preprocess data for RASQUAL analysis for caQTL calling 
+# Updated Jan 2026
+
 options(scipen = 100)
 library(data.table)
 library(readr)
diff --git a/QTLs/002_runRasqual.sh b/QTLs/002_runRasqual.sh
@@ -1,3 +1,6 @@
+# Script to run RASQUAL on SGE server
+# Updated Jan 2026
+
 #!/bin/bash
 #$ -S /bin/bash
 #$ -cwd
diff --git a/QTLs/003_runTensoqtl_sge.sh b/QTLs/003_runTensoqtl_sge.sh
@@ -1,3 +1,6 @@
+# Script to run TensorQTL on SGE server across cell types
+# Updated Jan 2026
+
 #!/bin/bash
 #$ -S /bin/bash
 #$ -N tensorQTL_job
diff --git a/QTLs/004_Fig3_eQTL.R b/QTLs/004_Fig3_eQTL.R
@@ -1,3 +1,6 @@
+# Script for Fig3 QTL plotting statistics
+# Updated Jan 2026
+
 library(data.table)
 library(qvalue)
 library(ArchR)
diff --git a/QTLs/005_Fig3_rs33_allelicimbalance.R b/QTLs/005_Fig3_rs33_allelicimbalance.R
@@ -1,3 +1,6 @@
+# rs33 allelilc imbalance script and plotting
+# Updated Jan 2026
+
 library(data.table)
 
 celltypes <- c("Microglia", "Astrocyte", "Oligo", "Granule")
diff --git a/RVAT/001_runSKAT_gnomad_gene.R b/RVAT/001_runSKAT_gnomad_gene.R
@@ -2,6 +2,7 @@
 
 # SKATO Analysis R Script
 # Converted from SGE batch script
+# Updated Jan 2026
 
 # Load required libraries
 library(data.table)
diff --git a/RVAT/002_skat_peak_gnomad_maf.sh b/RVAT/002_skat_peak_gnomad_maf.sh
@@ -1,3 +1,6 @@
+# Script used to run SKATO analysis for peak based variant grouping 
+# Updated Jan 2026 
+
 #!/bin/bash
 #$ -N skato_peak_analysis
 #$ -cwd
diff --git a/RVAT/003_mirrored_lollipop.R b/RVAT/003_mirrored_lollipop.R
@@ -1,3 +1,5 @@
+# Function to plot lollipop plots from RVAT results 
+# Updated Jan 2026 
 
 plot_gene_lollipop_from_files <- function(
     variants_path,

Original file line number	Diff line number	Diff line change
`@@ -1,3 +1,5 @@`
	`1`	`+# Plotting QC statistics -- specificially about sex and age of the cohort`
	`2`	`+# Updated Jan 2026`
`1`	`3`
`2`	`4`	`setwd("/gladstone/corces/lab/users/smenon/2304_PDMultiome_Final/Final_Objects/Scripts/Figure_Plotting/")`
`3`	`5`	`source("plotting_helper_corces.R")`