In Seurat, how can I export cluster IDs to csv files

Question

I am doing scRNAseq analysis with Seurat.

I clustered the cells using the FindClusters() function.

What I want to do is to export information about which cells belong to which clusters to a CSV file.

In a Seurat object, we can show the cluster IDs by using Idents(・), but I have no idea how to export this to CSV files.

I would be grateful if you could show this by using the PMBC data (https://satijalab.org/seurat/articles/pbmc3k_tutorial.html) as an example.

Answer 1

The clusters information, together with additional information on each cells (%mito, sample name, group, orig.ident,...) are stored inside [email protected]. write.csv([email protected],"./seurat_metadata.csv") will dump everything to a file.

The method @osmoc suggested, is using built in seurat functions to interact with [email protected]. seuratObject$graph_name_resolution points to [email protected]$graph_name_resolution.

I personally prefer to use the metadata table, as I have more control on how I interact with the data.

Answer 2

I've recently done this with my own Seurat data; here's the process:

# load tidyverse packages
library(tidyverse)
# create cluster ID table
tibble(cellID = colnames(pbmc), clusterID = Idents(pbmc)) %>%
  # write out to a file, with today's date
  write_csv(file = sprintf("cluster_mappings_%s.csv", Sys.Date()))

Answer 3

The clusters are saved in the field object$seurat_clusters where object represents your Seurat object.

You can also get them running the command Idents(object).

NOTE: if you run the command FindClusters on different SNN graphs, or different resolutions, you need to specify the clusters by object$graph_name_resolution. Every time you run FindClusters, the idents of the cells are updated to the latest results, same for seurat_clusters.

For instance, let's say that you have run the command FindNeighbors on the RNA assay (default value).
Then you run FindClusters with graph = "RNA_snn" and resolution=1.
In that case, the clusters are in object$RNA_snn_1.

Once you have the clusters, you can save them as a CSV:

clusters <-  <here you use one of the described methods>
# data.frame
clust.df <- data.frame(cellID = colnames(object), clusters = clusters)
write.csv(clust.df, <path.of.the.csv.file>)