Figure 4F

Code

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

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

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")

Code

p <- SCpubr::do_DimPlot(sample = sample,
                        group.by = "final_annotation",
                        font.size = 20,
                        raster = TRUE,
                        raster.dpi = 2048,
                        pt.size = 4,
                        colors.use = cluster_cols,
                        legend.icon.size = 8,
                        legend.ncol = 2,
                        na.value = "grey90")