--- a
+++ b/Fig5F_VISTA_IHC_boxplot.R
@@ -0,0 +1,44 @@
+
+# Plot IHC percentages of VISTA+ cells in different hematological cancers (Figure 5F)
+
+library(data.table)
+library(ggplot2)
+library(cowplot)
+library(ComplexHeatmap)
+library(dplyr)
+library(ggpubr)
+
+# read mIHC data
+data <- fread("vista_ihc.txt", data.table = F)
+
+# prepare data frame for plotting
+df <- data %>%
+  mutate(Disease_2 = gsub("BP CML", "CML", 
+                          gsub("PH. B-ALL", "pre-B-ALL", 
+                               gsub("HB", "Healthy BM", Disease))),
+         VISTA = VISTA.fraction*100) %>%
+  mutate(Disease_2 = ifelse(FAB %in% c("4", "5"), "AML M4/M5", 
+                            ifelse(Disease_2 == "AML", "AML other", Disease_2))) %>% 
+  mutate(Disease_2 = factor(Disease_2, levels = c("AML M4/M5", "AML other", "CML", "pre-B-ALL", "T-ALL", "Healthy BM")))
+         
+# boxplot
+p <- ggplot(df, aes(x=Disease_2, y=VISTA, fill = Disease_2)) +
+ geom_boxplot(outlier.shape = NA) +
+ geom_jitter(width = 0.1, color = "grey20") +
+ scale_size_continuous(range = c(0.1, 2)) +
+ ylab("% VISTA+ cells") +
+ xlab("") +
+ guides(fill = FALSE) +
+  theme_cowplot() +
+ theme(axis.text.x = element_text(angle=45, hjust=1)) +
+ labs(color = "") +
+ stat_compare_means(aes(label = ..p.signif..),
+   method = "wilcox.test",
+   method.args = list(alternative = "two.sided"),
+   ref.group = "Healthy BM",
+   label.y = 95)
+
+# print
+pdf("Figure5F_VISTA_IHC_boxplot.pdf", width = 3, height = 4)
+p
+dev.off()