Figure 1I

Code

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

# Load samples.
sample <- readRDS("/omics/odcf/analysis/OE0145_projects/idh_gliomas/Figures_Science/revision/IDH_gliomas_book/datasets/integrated_LGGs.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")
sample <- sample[, sample$relabelling %in% idents.keep]

Code

p0 <- SCpubr::do_BarPlot(sample = sample[, sample$subtype == "Oligodendroglioma"],
                         group.by = "relabelling",
                         split.by = "orig.ident",
                         facet.by = "subtype",
                         font.size = 18,
                         flip = TRUE,
                         colors.use = cluster_cols,
                         position = "fill",
                         legend.position = "none",
                         order = TRUE,
                         order.by = "RE",
                         plot.grid = FALSE,
                         add.n = TRUE,
                         add.n.expand = c(0, 1.15),
                         axis.text.face = "plain",
                         add.n.size = 5) +
      ggplot2::xlab("OD") +
      ggplot2::ylab("") + 
      ggplot2::theme(axis.text.x = ggplot2::element_blank(),
                     axis.ticks.x = ggplot2::element_blank(),
                     strip.text = ggplot2::element_blank(),
                     plot.margin = ggplot2::margin(t = 0, r = 10, b = 0, l = 10)) 

p1 <- SCpubr::do_BarPlot(sample = sample[, sample$subtype == "Astrocytoma"],
                         group.by = "relabelling",
                         split.by = "orig.ident",
                         facet.by = "subtype",
                         font.size = 18,
                         flip = TRUE,
                         colors.use = cluster_cols,
                         position = "fill",
                         legend.position = "none",
                         order = TRUE,
                         order.by = "RE",
                         plot.grid = FALSE,
                         add.n = TRUE,
                         add.n.expand = c(0, 1.15),
                         axis.text.face = "plain",
                         add.n.size = 5) +
      ggplot2::xlab("AS") +
      ggplot2::ylab("") + 
      ggplot2::theme(axis.text.x = ggplot2::element_blank(),
                     axis.ticks.x = ggplot2::element_blank(),
                     strip.text = ggplot2::element_blank(),
                     plot.margin = ggplot2::margin(t = 0, r = 10, b = 0, l = 10)) 

p2 <- SCpubr::do_BarPlot(sample = sample,
                         group.by = "relabelling",
                         split.by = "grade",
                         font.size = 18,
                         flip = TRUE,
                         colors.use = cluster_cols,
                         position = "fill",
                         order = FALSE,
                         plot.grid = FALSE,
                         legend.title = "",
                         add.n = TRUE,
                         add.n.expand = c(0, 1.15),
                         axis.text.face = "plain",
                         add.n.size = 5,
                         legend.ncol = 5) +
      ggplot2::xlab("Grade") +
      ggplot2::theme(plot.margin = ggplot2::margin(t = 0, r = 30, b = 0, l = 10))

layout <- paste(c(rep("A", 8), rep("B", 6), rep("C", 2), "D"), collapse = "\n")

p <- patchwork::wrap_plots(A = p0,
                           B = p1,
                           C = p2,
                           D = patchwork::guide_area(),
                           design = layout)