# Overarching Seurat object.
path.to.sample <- "path_to_snRNAseq_sample"
sample <- readRDS(path.to.sample)
orig.colors <- c("ATRT-TYR-1" = "#feac81",
"ATRT-TYR-2" = "#f78462",
"ATRT-TYR-3" = "#b9563f",
"ATRT-TYR-4" = "#f05b43",
"ATRT-TYR-5" = "#c62320",
"ATRT-TYR-6" = "#831818",
"ATRT-SHH-1" = "#abc9c8",
"ATRT-SHH-2" = "#72aeb6",
"ATRT-SHH-3" = "#4692b0",
"ATRT-SHH-4" = "#2f70a1",
"ATRT-SHH-5" = "#bad6f9",
"ATRT-SHH-6" = "#7db0ea",
"ATRT-SHH-7" = "#447fdd",
"ATRT-SHH-8" = "#134b73",
"ATRT-SHH-9" = "#0a3351",
"ATRT-MYC-1" = "#c2d6a4",
"ATRT-MYC-2" = "#9cc184",
"ATRT-MYC-3" = "#3c7c3d",
"ATRT-MYC-4" = "#1f5b25")
subtype.colors <- c("ATRT-TYR" = "#87191c",
"ATRT-SHH" = "#243a76",
"ATRT-MYC" = "#096837")
# Figure S1A ---------
sample$TME <- ifelse(sample$seurat_clusters %in% c("20", "19", "16", "13"), "TME", "Tumor")
sample$ID <- factor(sample$ID, levels = names(orig.colors))
p <- SCpubr::do_BarPlot(sample,
group.by = "ID",
split.by = "unintegrated_clusters",
facet.by = "TME",
font.size = 16,
colors.use = orig.colors,
position = "fill",
flip = TRUE,
xlab = "Clusters",
legend.ncol = 4)
# Figure S1B ---------
path.to.TME.markers <- "path_to_TME_markers"
markers <- readRDS(path.to.TME.markers)
p <- SCpubr::do_EnrichmentHeatmap(sample = sample[, sample$unintegrated_clusters %in% c("20", "19", "16", "13")],
input_gene_list = markers,
group.by = "unintegrated_clusters",
flavor = "UCell",
flip = TRUE,
font.size = 16,
cluster = TRUE) +
ggplot2::xlab("Clusters")
# Figure S1C ---------
p <- SCpubr::do_DimPlot(sample,
group.by = "subtype",
reduction = "umap_unintegrated",
font.size = 16,
raster = TRUE,
raster.dpi = 2048,
pt.size = 8,
colors.use = subtype.colors,
legend.icon.size = 8,
legend.ncol = 3,
legend.position = "bottom")
# Figure S1D ---------
path.to.CNV.scores <- "path_to_CNV_scores"
scores <- readRDS(path.to.CNV.scores)
out <- SCpubr::do_CopyNumberVariantPlot(sample = sample,
infercnv_object = scores,
chromosome_locations = SCpubr::human_chr_locations,
using_metacells = TRUE,
metacell_mapping = sample$metacell_mapping,
return_object = TRUE)
sample <- out$Object
p <- SCpubr::do_FeaturePlot(sample,
features = "22",
enforce_symmetry = TRUE,
symmetry.type = "centered",
symmetry.center = 1,
reduction = "umap_unintegrated",
font.size = 16,
max.cutoff = 1.1,
min.cutoff = 0.9,
legend.title = "Chr. 22 CNV score",
raster = TRUE,
raster.dpi = 2048,
pt.size = 8,
legend.position = "bottom")
# Figure S1F ---------
markers <- list("ATRT-TYR" = c("TYR", "MITF", "OTX2", "LMX1A", "PRRX1", "MSX2", "BMP4", "PDGFRB"),
"ATRT-SHH" = c("HES1", "GLI2", "BOC", "ASCL1", "HES5", "MYCN", "PTCH1", "DTX1", "CBL"),
"ATRT-MYC" = c("MYC", "CEBPB", "HOTAIR", "MYO1C"))
p1 <- SCpubr::do_DotPlot(sample,
features = markers,
font.size = 16,
group.by = "subtype")