Top Marker Expression by Cluster
Eileen Owens
2025-02-01
Software
library(Seurat)
library(tidyverse)
library(patchwork)
library(pheatmap)
library(RColorBrewer)
library(data.table)
library(knitr)
library(presto)Data
Input: Pre-processed Seurat object of integrated thymocyte and T-cell subsets from canine thymus and lymph node.
setwd("/Users/eileen/PTCL/Single-cell-RNA-seq")
all_Tcells <- readRDS(file = "integrated_Tcells.Rdata")
all_Tcells <- FindNeighbors(all_Tcells, dims = 1:10)
all_Tcells <- FindClusters(all_Tcells, resolution = 0.2)
all_Tcells <- RunUMAP(all_Tcells, dims = 1:10)
DimPlot(all_Tcells,
reduction = "umap",
group.by = "OriginalClusters",
label = TRUE,
label.size = 3,
label.box = TRUE) + plot_annotation(title= "Merged Canine T cells from Lymph Node and Thymus,\nOriginal Cluster IDs")
Cluster 0 markers
FeaturePlot(all_Tcells,
reduction = "umap",
features = c("HOPX", "SELL", "CCR7", "TRIM22", "DLA-DRA", "LTB", "HLA-DQB2", "LY6E")) +
plot_annotation(title = "Merged Canine T-cells from Lymph Node and Thymus:\nTop Cluster 0 Markers", theme = theme(plot.title = element_text(hjust = 0.5, size = 20))) &
scale_color_gradientn(colours = brewer.pal(name = "RdPu", n=11))
Cluster 1 markers
FeaturePlot(all_Tcells,
reduction = "umap",
features = c("RAG1", "DNTT", "CD1C", "PDE1C", "NT5DC2", "CD4", "CD8A", "THEMIS")) +
plot_annotation(title = "Merged Canine T-cells from Lymph Node and Thymus:\nTop Cluster 1 Markers", theme = theme(plot.title = element_text(hjust = 0.5, size = 20))) &
scale_color_gradientn(colours = brewer.pal(name = "RdPu", n=11))
Cluster 2 markers
FeaturePlot(all_Tcells,
reduction = "umap",
features = c("SELL", "LY6E", "CTLA4", "LTB", "IL2RA", "MAF", "S100A8", "ICOS")) +
plot_annotation(title = "Merged Canine T-cells from Lymph Node and Thymus:\nTop Cluster 2 Markers", theme = theme(plot.title = element_text(hjust = 0.5, size = 20))) &
scale_color_gradientn(colours = brewer.pal(name = "RdPu", n=11))
Cluster 3 markers
FeaturePlot(all_Tcells,
reduction = "umap",
features = c("RAG1", "DNTT", "CD1C", "SLC7A11", "DBX2", "CD4", "CD8A", "ADAM12", "ARRP21", "PDE1C", "THEMIS")) +
plot_annotation(title = "Merged Canine T-cells from Lymph Node and Thymus:\nTop Cluster 3 Markers", theme = theme(plot.title = element_text(hjust = 0.5, size = 20))) &
scale_color_gradientn(colours = brewer.pal(name = "RdPu", n=11))
Cluster 4 markers
FeaturePlot(all_Tcells,
reduction = "umap",
features = c("CCR9", "ASAP1", "CELF2", "TOX2", "GATA3", "THEMIS")) +
plot_annotation(title = "Merged Canine T-cells from Lymph Node and Thymus:\nTop Cluster 4 Markers", theme = theme(plot.title = element_text(hjust = 0.5, size = 20))) &
scale_color_gradientn(colours = brewer.pal(name = "RdPu", n=11))
Cluster 5 markers
FeaturePlot(all_Tcells,
reduction = "umap",
features = c("SELL", "CCR7", "TGFBR2", "INPP4B", "PDE3B", "SCML4", "RIPOR2", "TRIM22", "ITGA1")) +
plot_annotation(title = "Merged Canine T-cells from Lymph Node and Thymus:\nTop Cluster 5 Markers", theme = theme(plot.title = element_text(hjust = 0.5, size = 20))) &
scale_color_gradientn(colours = brewer.pal(name = "RdPu", n=11))
Cluster 6 markers
FeaturePlot(all_Tcells,
reduction = "umap",
features = c("MKI67", "DNTT", "CD1C", "TPX2", "KNL1", "CD4", "CD8A", "SMC2", "DIAPH3", "THEMIS")) +
plot_annotation(title = "Merged Canine T-cells from Lymph Node and Thymus:\nTop Cluster 6 Markers", theme = theme(plot.title = element_text(hjust = 0.5, size = 20))) &
scale_color_gradientn(colours = brewer.pal(name = "RdPu", n=11))
Cluster 7 markers
FeaturePlot(all_Tcells,
reduction = "umap",
features = c("LY6E", "LTB", "KLRB1", "IL2RB", "CD160", "CD96", "KLRK1", "GZMA")) +
plot_annotation(title = "Merged Canine T-cells from Lymph Node and Thymus:\nTop Cluster 7 Markers", theme = theme(plot.title = element_text(hjust = 0.5, size = 20))) &
scale_color_gradientn(colours = brewer.pal(name = "RdPu", n=11))
Cluster 8 markers
FeaturePlot(all_Tcells,
reduction = "umap",
features = c("RAG1", "DNTT", "KIT", "ALPL", "MKI67", "ASNS", "DPP4", "CDH1", "HDAC4", "NDST3", "THEMIS")) +
plot_annotation(title = "Merged Canine T-cells from Lymph Node and Thymus:\nTop Cluster 8 Markers", theme = theme(plot.title = element_text(hjust = 0.5, size = 20))) &
scale_color_gradientn(colours = brewer.pal(name = "RdPu", n=11))
FeaturePlot(all_Tcells,
reduction = "umap",
features = c("CD4", "CD8A")) +
plot_annotation(title = "CD4 and CD8 Expression in Cluster 8", theme = theme(plot.title = element_text(hjust = 0.5, size = 20))) &
scale_color_gradientn(colours = brewer.pal(name = "RdPu", n=11))
Cluster 9 markers
FeaturePlot(all_Tcells,
reduction = "umap",
features = c("LY6E", "LGALS3", "KLRB1", "IL2RA", "RARRES2", "RPS6KA2", "RORA", "DSTN", "DENND5A", "MAF", "S100A8", "CD7")) +
plot_annotation(title = "Merged Canine T-cells from Lymph Node and Thymus:\nTop Cluster 9 Markers", theme = theme(plot.title = element_text(hjust = 0.5, size = 20))) &
scale_color_gradientn(colours = brewer.pal(name = "RdPu", n=11))
Cluster 10 markers
FeaturePlot(all_Tcells,
reduction = "umap",
features = c("HAVCR1", "HAVCR2", "RBPMS", "SOX5", "BCL2", "CCR9", "CD7")) +
plot_annotation(title = "Merged Canine T-cells from Lymph Node and Thymus:\nTop Cluster 10 Markers", theme = theme(plot.title = element_text(hjust = 0.5, size = 20))) &
scale_color_gradientn(colours = brewer.pal(name = "RdPu", n=11))
Citations
sessionInfo()## R version 4.4.0 (2024-04-24)
## Platform: aarch64-apple-darwin20
## Running under: macOS Sonoma 14.6.1
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## time zone: America/Denver
## tzcode source: internal
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] presto_1.0.0 Rcpp_1.0.14 knitr_1.47 data.table_1.16.4
## [5] RColorBrewer_1.1-3 pheatmap_1.0.12 patchwork_1.2.0 lubridate_1.9.3
## [9] forcats_1.0.0 stringr_1.5.1 dplyr_1.1.4 purrr_1.0.2
## [13] readr_2.1.5 tidyr_1.3.1 tibble_3.2.1 ggplot2_3.5.1
## [17] tidyverse_2.0.0 Seurat_5.2.0 SeuratObject_5.0.2 sp_2.1-4
##
## loaded via a namespace (and not attached):
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## [22] igraph_2.0.3 mime_0.12 lifecycle_1.0.4
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## [49] tools_4.4.0 lmtest_0.9-40 httpuv_1.6.15
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## [73] later_1.3.2 splines_4.4.0 lattice_0.22-6
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## [103] viridisLite_0.4.2 scales_1.3.0 ggridges_0.5.6
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