Code Availability

Code used in Supplementary Figure 6: 

# Load necessary libraries

library(Seurat)

library(Matrix)

library(ggplot2)

# Load barcodes, features, and expression matrix

barcodes <- read.table(gzfile('barcodes.tsv.gz'), header = FALSE, stringsAsFactors = FALSE)

features <- read.table(gzfile('features.tsv.gz'), header = FALSE, stringsAsFactors = FALSE)

expression_matrix <- readMM(gzfile('matrix.mtx.gz'))

# Load cell annotations

cluster_membership <- read.csv('cluster.membership.csv')

cluster_annotation <- read.csv('cluster.annotation.csv')

# Merge the cluster membership and annotation to get cell type info

merged_df <- merge(cluster_membership, cluster_annotation, by.x = "x", by.y = "cluster_id", all.x = TRUE)

# Filter for glial cells (Astrocytes and Microglia)

glial_cells <- merged_df[grep("Astro|Macrophage|Oligo|OPC|Endo", merged_df$subclass_label, ignore.case = TRUE), ]

write.csv(glial_cells, "glial_cells.csv", row.names = FALSE)

# Trim white spaces from barcodes and ensure barcodes match

# Remove rows with NA or empty values

barcodes <- barcodes[!is.na(barcodes$V1) & barcodes$V1 != "", ]

barcodes_col <- trimws(barcodes$V2)  # Barcodes from the expression matrix

# Clean the barcodes_col by removing the leading commas and quotes

barcodes_col_clean <- gsub('^,"|"$', '', barcodes_col)

# Check if the cleaning worked

head(barcodes_col_clean)

glial_barcodes <- trimws(glial_cells$X)  # Barcodes from glial cells

head(barcodes_col)

head(glial_barcodes)

# Match the barcodes between the glial cells and expression matrix

matched_barcodes_idx <- match(glial_barcodes, barcodes_col_clean)

# Subset the expression matrix to include only the glial cells

subset_expression_matrix <- expression_matrix[, matched_barcodes_idx]

# Find the row corresponding to Ptgs1 in the features file

pts1_row <- grep("Ptgs1", features$V2, ignore.case = TRUE)

# Extract Ptgs1 expression for the glial cells

pts1_expression <- subset_expression_matrix[pts1_row, , drop = FALSE]

pts1_expression <- as.numeric(pts1_expression)

# Check if the number of glial cells matches the length of the expression vector

if (nrow(glial_cells) == length(pts1_expression)) {

  glial_cells$Ptsg1_expression <- pts1_expression

} else {

  stop("Mismatch between the number of glial cells and the length of Ptgs1 expression data.")

}

# Plot the Ptgs1 expression in glial cells

ggplot(glial_cells, aes(x = subclass_label, y = Ptsg1_expression)) +

  geom_bar(stat = "identity", fill = "steelblue") +

  theme_minimal() +

  labs(title = "Ptgs1 Gene Expression in Glial Cells", x = "Cell Type", y = "Expression Level") +

  theme(axis.text.x = element_text(angle = 45, hjust = 1))

# Change "Macrophage" to "Microglia/Macrophage" in the subclass_label column

glial_cells$subclass_label <- gsub("Macrophage", "Microglia/Macrophage", glial_cells$subclass_label)

# Reorder subclass_label factor levels to put Microglia/Macrophage first, Endo second, and Astro third

glial_cells$subclass_label <- factor(glial_cells$subclass_label, 

                                     levels = c("Microglia/Macrophage", "Endo", "Astro", "Oligo", "OPC"))

# Create the plot with the new order

ggplot(glial_cells, aes(x = subclass_label, y = Ptsg1_expression, fill = subclass_label)) +

  geom_bar(stat = "identity") +

  theme_minimal() +  # Minimal theme to remove unnecessary background elements

  theme(panel.grid = element_blank(),   # Remove background grid lines

        axis.line = element_line(),     # Add axis lines

        axis.text.x = element_text(angle = 45, hjust = 1)) +  # Rotate x-axis labels

  scale_fill_manual(values = c("Astro" = "gray", "Endo" = "magenta", 

                               "Microglia/Macrophage" = "green3")) +  # Change colors for specific categories

  labs(title = "Ptgs1- Mus musculus", 

       x = "Cell Type", 

       y = "FPKM")

This is your Project description. A brief summary can help visitors understand the context of your work. Click on "Edit Text" or double click on the text box to start.

This is your Project description. Provide a brief summary to help visitors understand the context and background of your work. Click on "Edit Text" or double click on the text box to start.

This is your Project description. Click on "Edit Text" or double click on the text box to start.

This is your Project description. Provide a brief summary to help visitors understand the context and background of your work. Click on "Edit Text" or double click on the text box to start.

This is your Project description. A brief summary can help visitors understand the context of your work. Click on "Edit Text" or double click on the text box to start.