Figure S7A

Code

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

sample <- readRDS("/omics/odcf/analysis/OE0145_projects/idh_gliomas/Figures_Science/revision/IDH_gliomas_book/datasets/primary_ATAC_OD.rds")

scale.ident <- c("IDH_ACB_AD_809" = "#F2CC8F",
                 "IDH_ACB_AD_883" = "#DAA82B",
                 "IDH_NCH2111" = "#81B29A",
                 "IDH_NCH6341" = "#5CADC1")

sample$orig.ident <- stringr::str_replace_all(sample$orig.ident, "OE0145-", "")

Code

p1 <- SCpubr::do_ViolinPlot(sample = sample,
                            group.by = "orig.ident",
                            features = "percentage_reads_in_peaks",
                            colors.use = scale.ident,
                            boxplot_width = 0.05,
                            font.size = 20,
                            axis.text.face = "plain") + 
      ggplot2::labs(y = "Pct. Reads in Peaks",
                    x = "") +
      ggplot2::theme(axis.text.x = ggplot2::element_blank(),
                     axis.ticks.x = ggplot2::element_blank(),
                     axis.title.x = ggplot2::element_blank())

p2 <- SCpubr::do_ViolinPlot(sample = sample,
                            group.by = "orig.ident",
                            features = "peak_region_fragments",
                            colors.use = scale.ident,
                            boxplot_width = 0.05,
                            font.size = 20,
                            axis.text.face = "plain") + 
      ggplot2::labs(y = "Peak region fragments",
                    x = "") +
      ggplot2::theme(axis.text.x = ggplot2::element_blank(),
                     axis.ticks.x = ggplot2::element_blank(),
                     axis.title.x = ggplot2::element_blank())

p3 <- SCpubr::do_ViolinPlot(sample = sample,
                            group.by = "orig.ident",
                            features = "blacklist_ratio",
                            colors.use = scale.ident,
                            boxplot_width = 0.05,
                            font.size = 20,
                            axis.text.face = "plain") + 
      ggplot2::labs(y = "Blacklist ratio",
                    x = "") +
      ggplot2::scale_y_continuous(limits = c(0, 0.0075)) +
      ggplot2::theme(axis.text.x = ggplot2::element_blank(),
                     axis.ticks.x = ggplot2::element_blank(),
                     axis.title.x = ggplot2::element_blank())

p4 <- SCpubr::do_ViolinPlot(sample = sample,
                            group.by = "orig.ident",
                            features = "TSS.enrichment",
                            colors.use = scale.ident,
                            boxplot_width = 0.05,
                            font.size = 20,
                            axis.text.face = "plain") + 
      ggplot2::labs(y = "TSS enrichment",
                    x = "") +
      ggplot2::theme(axis.text.x = ggplot2::element_blank(),
                     axis.ticks.x = ggplot2::element_blank(),
                     axis.title.x = ggplot2::element_blank())

p5 <- SCpubr::do_ViolinPlot(sample = sample,
                            group.by = "orig.ident",
                            features = "nucleosome_signal",
                            colors.use = scale.ident,
                            boxplot_width = 0.05,
                            font.size = 20,
                            axis.text.face = "plain") + 
      ggplot2::labs(y = "Nucleosome signal",
                    x = "Patient") +
      ggplot2::scale_y_continuous(limits = c(0, 0.75))

p <- p1 / p2 / p3 / p4 / p5