Figure S4C

Code

sample.oligo <- readRDS("/omics/odcf/analysis/OE0145_projects/idh_gliomas/Figures_Science/revision/IDH_gliomas_book/datasets/integrated_primary_OD.rds")
sample.oligo$orig.ident <- stringr::str_remove_all(sample.oligo$orig.ident, "OE0145-")

scale.ident <- c("IDH_ACB_AD_540" = "#E07A5F",
                 "IDH_ACB_AD_809" = "#F2CC8F",
                 "IDH_ACB_AD_883" = "#DAA82B",
                 "IDH_NCH2111" = "#81B29A",
                 "IDH_NCH536" = "#3E745E",
                 "IDH_NCH6341" = "#5CADC1",
                 "IDH_NCH6702" = "#8B6BB8",
                 "IDH_NCH781" = "#3D405B")

# Define set of markers.
markers.suva <- readRDS("/omics/odcf/analysis/OE0145_projects/idh_gliomas/Figures_Science/revision/IDH_gliomas_book/datasets/IDH_gliomas_TB_annotation_kit_with_Suva_programs_and_metaprogram_iterations.rds")

sample.oligo <- SCpubr:::compute_enrichment_scores(sample = sample.oligo,
                                                   input_gene_list = list("Stemness_program" = markers.suva$Suva_Stemness_Program),
                                                   flavor = "Seurat")

Code

p <- SCpubr::do_BoxPlot(sample = sample.oligo[, sample.oligo$relabelling == "RA"],
                        feature = "Stemness_program",
                        order = TRUE,
                        group.by = "orig.ident",
                        colors.use = scale.ident,
                        font.size = 20,
                        axis.text.face = "plain") +
     ggplot2::ylab("Stemness enrichment score") +
     ggplot2::xlab("Patient")