Figure S8D

Code

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

# Read in sample.
sample <- readRDS("/omics/odcf/analysis/OE0145_projects/idh_gliomas/Figures_Science/revision/IDH_gliomas_book/datasets/microglia_primary.rds")

# Define colors.
cluster_cols <- c("Mg Homeostatic"= "#ECA809",                          
                  "Mg Inflammatory TAMs" = "#043362",                  
                  "Mg Activated"= "#9A031E",                 
                  "Mg Resident−like TAMs"= "#009FF5",                    
                  "BMD Anti−inflammatory TAMs"= "#BC5210",            
                  "Mg Phagocytic"= "#279185",                 
                  "Mg IFNg TAMs"= "#7EB356",                   
                  "Mg Stressed TAMs"= "#AC70FF",                  
                  "Mg Inflammatory ICAM1+"= "#63412C",                  
                  "BAMs" = "#5F0F40")

scale.subtype.short <- c("Astrocytoma" = "#b38b14",
                         "Oligodendroglioma" = "#3c5b8b")


markers <- readr::read_tsv("/omics/odcf/analysis/OE0145_projects/idh_gliomas/Figures_Science/revision/IDH_gliomas_book/datasets/TAM_markers.tsv")
markers <- lapply(as.list(markers), function(x){x[!is.na(x)]})
markers <- markers[c("Pro-Inflammatory", "Anti-Inflammatory")]
names(markers) <- c("Pro_Inflammatory", "Anti_Inflammatory")

sample <- SCpubr:::compute_enrichment_scores(sample = sample,
                                             input_gene_list = markers,
                                             flavor = "UCell",
                                             assay = "RNA")
sample$subtype <- factor(sample$subtype, levels = c("Oligodendroglioma", "Astrocytoma"))

Code

p1 <- SCpubr::do_BoxPlot(sample,
                         feature = "Pro_Inflammatory",
                         group.by = "final_annotation",
                         split.by = "subtype",
                         colors.use = scale.subtype.short,
                         font.size = 20,
                         axis.text.face = "plain",
                         legend.position = "right",
                         legend.title = "LGG subtype") + 
      ggplot2::ylab("Pro Inflammatory TAMs") + 
      ggplot2::xlab("") +
      ggplot2::scale_y_continuous(limits = c(0, 0.25)) +
      ggplot2::theme(axis.text.x = ggplot2::element_blank(),
                     axis.ticks.x = ggplot2::element_blank(),
                     axis.line.x = ggplot2::element_blank(),
                     legend.position = "none")

p2 <- SCpubr::do_BoxPlot(sample,
                         feature = "Anti_Inflammatory",
                         group.by = "final_annotation",
                         split.by = "subtype",
                         colors.use = scale.subtype.short,
                         font.size = 20,
                         axis.text.face = "plain",
                         legend.position = "right",
                         legend.title = "LGG subtype")  +
      ggplot2::scale_y_continuous(limits = c(0, 0.25)) +
      ggplot2::ylab("Anti Inflammatory TAMs") + 
      ggplot2::xlab("")


p3 <- SCpubr::do_BoxPlot(sample,
                         feature = "Pro_Inflammatory",
                         group.by = "subtype",
                         colors.use = scale.subtype.short,
                         font.size = 20,
                         axis.text.face = "plain",
                         legend.position = "right",
                         legend.title = "LGG subtype") +
      ggplot2::scale_y_continuous(limits = c(0, 0.25)) + 
      ggplot2::ylab("") + 
      ggplot2::xlab("") +
      ggplot2::theme(axis.text.x = ggplot2::element_blank(),
                     axis.ticks.x = ggplot2::element_blank(),
                     axis.line.x = ggplot2::element_blank(),
                     axis.text.y = ggplot2::element_blank(),
                     axis.ticks.y = ggplot2::element_blank(),
                     axis.line.y = ggplot2::element_blank(),
                     legend.position = "none")

p4 <- SCpubr::do_BoxPlot(sample,
                          feature = "Anti_Inflammatory",
                          group.by = "subtype",
                          colors.use = scale.subtype.short,
                          font.size = 20,
                          axis.text.face = "plain",
                         legend.position = "right",
                         legend.title = "LGG subtype") +  
      ggplot2::scale_y_continuous(limits = c(0, 0.25)) + 
      ggplot2::ylab("") + 
      ggplot2::xlab("") + 
      ggplot2::theme(axis.text.y = ggplot2::element_blank(),
                     axis.ticks.y = ggplot2::element_blank(),
                     axis.line.y = ggplot2::element_blank())

layout <- "AAAAAAAAAAAAAAAAAAAACCE
           BBBBBBBBBBBBBBBBBBBBDDE"
p <- patchwork::wrap_plots(A = p1,
                           B = p2,
                           C = p3,
                           D = p4,
                           E = patchwork::guide_area(),
                           guides = "collect",
                           design = layout)