Figure S10B

Code

# Enrique Blanco Carmona
# e.blancocarmona@kitz-heidelberg.de
# PhD Student – Clinical Bioinformatics
# Division of Pediatric Neurooncology (B062)
# DKFZ-KiTZ | Germany

# Read in metadata.
sample <- readRDS("/omics/odcf/analysis/OE0145_projects/idh_gliomas/Figures_Science/revision/IDH_gliomas_book/datasets/integrated_paired_AS.rds")
sample$relabelling[sample$relabelling == "RA"] <- "RE"
Seurat::Idents(sample) <- sample$relabelling

cluster_cols <- c("RE" = "#ECA809",
                  "OPC-like" = "#043362",                    
                  "Gradient" = "#D6D6D6",                    
                  "Astro-like" = "#9A031E",                  
                  "Cycling" = "#5F0F40")

idents.keep <- c("OPC-like", "Astro-like", "RE", "Gradient", "Cycling")

Code

p1 <- SCpubr::do_DimPlot(sample = sample,
                         idents.keep = idents.keep,
                         group.by = "relabelling",
                         font.size = 20,
                         raster = TRUE,
                         raster.dpi = 2048,
                         pt.size = 6,
                         colors.use = cluster_cols,
                         legend.icon.size = 8,
                         legend.ncol = 2,
                         na.value = "grey50")

p2 <- SCpubr::do_DimPlot(sample = sample,
                         split.by = "time",
                         font.size = 20,
                         raster = TRUE,
                         raster.dpi = 2048,
                         pt.size = 6,
                         colors.use = scale.status,
                         legend.icon.size = 8,
                         legend.ncol = 2,
                         na.value = "grey90")

p3 <- SCpubr::do_DimPlot(sample = sample,
                         split.by = "grade",
                         font.size = 20,
                         raster = TRUE,
                         raster.dpi = 2048,
                         pt.size = 6,
                         colors.use = scale.grade,
                         legend.icon.size = 8,
                         legend.ncol = 3,
                         na.value = "grey90")

layout <- c("ABB
             CCC")

p <- patchwork::wrap_plots(A = p1,
                           B = p2,
                           C = p3,
                           design = layout)