Figure S8B

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")

Code

out <- SCpubr:::compute_umap_layer(sample,
                                   labels = colnames(sample@reductions[["umap"]][[]])[1:2],
                                   border.color = "black",
                                   pt.size = 1,
                                   border.size = 2)

p1 <- SCpubr::do_NebulosaPlot(sample[, sample$subtype == "Astrocytoma"], 
                              features = "Anti_Inflammatory",
                              font.size = 20,
                              use_viridis = FALSE,
                              plot.title = "Anti Inflammatory TAMs | AS",
                              sequential.direction = 1) + ggplot2::theme(plot.title = ggplot2::element_text(face = "bold", hjust = 0.5))
p1$layers <- append(out$na_layer, p1$layers)
p1$layers <- append(out$base_layer, p1$layers)

p2 <- SCpubr::do_NebulosaPlot(sample[, sample$subtype == "Oligodendroglioma"], 
                              features = "Anti_Inflammatory",
                              font.size = 20,
                              use_viridis = FALSE,
                              plot.title = "Anti Inflammatory TAMs | OD",
                              sequential.direction = 1) + ggplot2::theme(plot.title = ggplot2::element_text(face = "bold", hjust = 0.5))
p2$layers <- append(out$na_layer, p2$layers)
p2$layers <- append(out$base_layer, p2$layers)

p <- p2 | p1