UMAP of TRA/B

Hello,

I have output from a single cell sequencing run that has both the VDJ and gene expression data. For the same cells, we also used a hybrid capture approach to sequence the TCR sequences. I have compared the TCR sequences across the two approaches and I have found a list of TRA and TRB cdr3 sequences that overlap. For the TRA sequences, there are 101 cells that were identified in both approaches. From here, I would like to use dimplot to look at a UMAP of where these cells fall in the clustering.

I have used the code below to integrate the vdj and gene expression data:

tcr <- read.csv(paste("/Users/carlygraham/Dropbox/BramsonLab/scRNAseq-Feb16/Multi_TAC_Output_v2/vdj/", "filtered_contig_annotations.csv", sep=""))

tcr <- tcr[!duplicated(tcr$barcode), ]

# Only keep the barcode and clonotype columns. 
# We'll get additional clonotype info from the clonotype table. 

tcr <- tcr[,c("barcode", "raw_clonotype_id")] 
names(tcr)[names(tcr) == "raw_clonotype_id"] <- "clonotype_id"

# Clonotype-centric info. 
clono <- read.csv(paste("/Users/carlygraham/Dropbox/BramsonLab/scRNAseq-Feb16/Multi_TAC_Output_v2/vdj/","clonotypes.csv", sep=""))

# Slap the AA sequences onto our original table by clonotype_id. 
tcr <- merge(tcr, clono[, c("clonotype_id", "cdr3s_aa")])

# Reorder so barcodes are first column and set them as rownames.
tcr <- tcr[, c(2,1,3)] 
rownames(tcr) <- tcr[,1] 
tcr[,1] <- NULL

# Add to the Seurat object's metadata. 
scRNAseq.seurat <- AddMetaData(object=scRNAseq.seurat, metadata=tcr) 

This effectively gives me a seurat object with the cdr3 as metadata

head(scRNAseq.seurat$cdr3s_aa)

AAACCTGAGCGTGTCC-1
“TRB:CASGRTGTYEQYF;TRA:CAAREGDKIIF;TRA:CASDAGNMLTF”
AAACCTGAGGCTCAGA-1
“TRB:CASSVPPGNTEAFF;TRA:CALSEGGLMYSGGGADGLTF;TRA:CAVGHSSGSARQLTF”
AAACCTGAGTGCGATG-1
“TRB:CSGKEGGMGTEAFF;TRA:CALSDRGSGNTPLVF”
AAACCTGCAAAGTGCG-1
“TRB:CASSEWGRGDTQYF;TRB:CASSHASIGNNEQFF;TRA:CAVRDQGRLMF;TRA:CAVTVNTNAGKSTF”
AAACCTGCAAGGGTCA-1
“TRB:CASSRGWRQETQYF;TRA:CAAPINFGNEKLTF”
AAACCTGCACGCGAAA-1
“TRB:CASSPTGRDNTEAFF;TRA:CAYGPPPAGNMLTF;TRA:CGAVNSGGYQKVTF”

From here is there a way to pull out some of the cells and display them on the UMAP?

Ex. pull out the cells with TRA:CAYGPPPAGNMLTF and TRA:CAAREGDKIIF?

Thanks!