Figure S10A

Code

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

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")

scale.grade <- c("Grade 2" = "#1a7d9e",
                 "Grade 3" = "#9e1a3b",
                 "Grade 4" = "#576e12")

scale.status <- c("Primary" = "#ee9b00",
                  "Relapse" = "#9b2226")

Code

p1 <- SCpubr::do_DimPlot(sample = sample,
                         group.by = "final_annotation",
                         font.size = 20,
                         raster = TRUE,
                         raster.dpi = 2048,
                         pt.size = 6,
                         colors.use = cluster_cols,
                         legend.icon.size = 8,
                         legend.ncol = 2,
                         na.value = "grey90")

p2 <- SCpubr::do_DimPlot(sample = sample,
                         split.by = "time",
                         font.size = 20,
                         raster = TRUE,
                         raster.dpi = 2048,
                         pt.size = 6,
                         colors.use = scale.status,
                         legend.icon.size = 8,
                         legend.ncol = 2,
                         na.value = "grey90")

p3 <- SCpubr::do_DimPlot(sample = sample,
                         split.by = "grade",
                         font.size = 20,
                         raster = TRUE,
                         raster.dpi = 2048,
                         pt.size = 6,
                         colors.use = scale.grade,
                         legend.icon.size = 8,
                         legend.ncol = 3,
                         na.value = "grey90")

layout <- c("ABB
             CCC")

p <- patchwork::wrap_plots(A = p1,
                           B = p2,
                           C = p3,
                           design = layout)