Figure 2G

Code

# Inma Hernandez Lopez
# inmaculada.hernandez-lopez@ukr.de
# LIT -  Leibniz-Institute für Immunotherapie

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


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

Seurat::DefaultAssay(sample.oligo) <- "ATAC"
Seurat::DefaultAssay(sample.astro) <- "ATAC"

sample.oligo <- sample.oligo[, sample.oligo$relabelling %in% c("OPC-like", "Astro-like", "RA", "Cycling")]
sample.astro <- sample.astro[, sample.astro$relabelling %in% c("OPC-like", "Astro-like", "RA", "Cycling")]
sample.oligo$relabelling[sample.oligo$relabelling == "RA"] <- "RE"
sample.astro$relabelling[sample.astro$relabelling == "RA"] <- "RE"


Seurat::Idents(sample.oligo) <- sample.oligo$relabelling
Seurat::Idents(sample.astro) <- sample.astro$relabelling

sample.oligo <- Seurat::FindVariableFeatures(sample.oligo)
sample.astro <- Seurat::FindVariableFeatures(sample.astro)

Code

p1 <- SCpubr::do_CorrelationPlot(sample.oligo,
                                 mode = "hvg",
                                 assay = "ATAC",
                                 max.cutoff = 0.5,
                                 min.cutoff = -0.5,
                                 font.size = 20,
                                 legend.length = 15,
                                 legend.width = 0.5,
                                 legend.framecolor = "grey50",
                                 legend.tickcolor = "white",
                                 legend.framewidth = 0.2,
                                 legend.tickwidth = 0.2,
                                 axis.text.face = "plain",
                                 legend.position = "none") + 
      ggplot2::xlab("OD")

p2 <- SCpubr::do_CorrelationPlot(sample.astro,
                                 mode = "hvg",
                                 assay = "ATAC",
                                 max.cutoff = 0.5,
                                 min.cutoff = -0.5,
                                 font.size = 20,
                                 legend.length = 15,
                                 legend.width = 0.5,
                                 legend.framecolor = "grey50",
                                 legend.tickcolor = "white",
                                 legend.framewidth = 0.2,
                                 legend.tickwidth = 0.2,
                                 axis.text.face = "plain")  + 
       ggplot2::xlab("AS")

p <- patchwork::wrap_plots(A = p1, B = p2, C = patchwork::guide_area(),design = "AB
                                                                                 CC", guides = "collect")