--- a
+++ b/Fig5E_PDL1_IHC_boxplot.R
@@ -0,0 +1,49 @@
+
+# Plot IHC percentages of PD-L1+ cells in different hematological cancers (Figure 5E)
+
+library(data.table)
+library(ggplot2)
+library(RColorBrewer)
+library(cowplot)
+library(dplyr)
+library(ggpubr)
+
+# read mIHC data
+data <- fread("pdl1_ihc.txt", data.table = F)
+
+# order cancers for plotting
+
+data <- data %>% 
+  mutate(Cancer_type = factor(Cancer_type, levels = c("DLBCL (non-GCB)", "DLBCL (GCB)", "pre-B-ALL", "T-ALL", "AML", "CML", "Healthy BM")))
+  
+# boxplot of all cancers with ABC and GCB separately
+p <- ggplot(data, aes(x = Cancer_type, y = PDL1, fill = Cancer_type)) +
+  geom_boxplot(outlier.shape = NA) +
+  geom_jitter(width = 0.1, color = "grey20") +
+  #geom_jitter(data = df[df$Subtype=="Blast phase CML",], aes(color = Subtype), width = 0.1) +
+  scale_size_continuous(range = c(0.1, 2)) +
+  scale_y_continuous(limits = c(-0.1,112), breaks = c(0, 25, 50, 75, 100)) +
+  ylab("% PD-L1+ cells") +
+  xlab("") +
+  guides(fill = FALSE) +
+  theme_cowplot() +
+  theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
+  scale_fill_manual(values = c("DLBCL (GCB)" = "rosybrown", "DLBCL (non-GCB)" = "rosybrown", "AML" = "mediumseagreen", "CML" = "darkgreen", "pre-B-ALL" = "violet", "T-ALL" = "cornflowerblue", "Healthy BM" = "grey50")) +
+  labs(color = "") +
+  stat_compare_means(ref.group = "Healthy BM",
+                     label = "p.signif",
+                     symnum.args = list(cutpoints = c(0, 0.0001, 0.001, 0.01, 0.05, 1), symbols = c("****", "***", "**", "*", "ns")),
+                     method = "wilcox.test",
+                     label.y = 112) +
+  stat_compare_means(comparisons = list(c("DLBCL (GCB)", "DLBCL (non-GCB)")),
+                     label = "p.signif",
+                     symnum.args = list(cutpoints = c(0, 0.0001, 0.001, 0.01, 0.05, 1), symbols = c("****", "***", "**", "*", "ns")),
+                     method = "wilcox.test",
+                     label.y = 105)
+
+
+
+# print
+pdf("Figure5E_PDL1_IHC_boxplot.pdf", width = 3, height = 4.25)
+p
+dev.off()