Histogram of normalized counts for each cell type

Question

[odi]

So,

I am visualizing wanting to make a histogram in R using my normalized counts (from SCTransform). Specifically, i want the y-axis to be normalized counts and the x-axis to be my seurat Idents (i have: A, B, C, D) and grouped by Wildtype (WT) and Mutant(MT).

Is this possible in R with seurat object as i do not really know how to retrieve this data to make my plot.

Thank you for the help everyone. I appreciate it

Answer 1

[bk11]

I'm showing for one gene only in this code, you can do similarly for other genes as well.

rm(list=ls())
library(Seurat)
library(SeuratData)
library(ggplot2)

seurat_obj=UpdateSeuratObject(pbmc3k.final)

# Add a new column 'condition' and assign values 'WT' and 'MT'
metadata <- data.frame(
  cell_id = colnames(seurat_obj),
  other_metadata_column = sample(c("Group1", "Group2"), ncol(seurat_obj), replace = TRUE)
)

# Assign the metadata to Seurat object
seurat_obj <- AddMetaData(object = seurat_obj, metadata = metadata)
[e-mail]$condition <- ifelse(metadata$other_metadata_column == "Group1", "WT", "MT")

# Print the updated metadata to verify
head([e-mail])

normalized_counts <- GetAssayData(seurat_obj, layer =  "data", assay = "RNA")

# Extract meta data
metadata <- [e-mail]

# Specify the gene of interest
gene_of_interest <- "MS4A1"

# Get the normalized counts for the specific gene
gene_data <- normalized_counts[gene_of_interest, ]

# Combine with metadata
plot_data <- data.frame(
  Seurat_Ident = Idents(seurat_obj),
  Condition = metadata$condition,  # Replace 'condition' with your actual column name in metadata
  Normalized_Count = gene_data
)

# Check the data
head(plot_data)

# Plot the histogram
ggplot(plot_data, aes(x = Seurat_Ident, y = Normalized_Count, fill = Condition)) +
  geom_histogram(stat = "identity", position = "dodge") +
  labs(title = paste("Normalized counts for", gene_of_interest),
       x = "Seurat Idents",
       y = "Normalized Counts") +
  theme_minimal() +
  scale_fill_manual(values = c("WT" = "blue", "MT" = "red"))

[odi]

I just saw this and wanted to say thank you. I am attempting to make this plot for TimePoint (metadata information) week 1 instead of a specific gene. Is that even possible?

[bk11]

Please see title of your question what had you asked for help. Now you are asking something else. You can get normalized counts for genes, right?? and not for week 1 or others...

[odi]

Yes, you are right! I just needed some confirmation. I am still just learning how to do single cell analysis so i mostly always have questions as there is something new. Thank you i really appreciated your answer.