--- a
+++ b/Fig6F_CoMMpass_CGA_boxplot.R
@@ -0,0 +1,63 @@
+
+# Plot boxplot of numbers of expressed CGAs in CoMMpass myeloma subtypes (Figure 6F)
+
+library(ggpubr)
+library(ggplot2)
+library(RColorBrewer)
+library(gridExtra)
+library(dplyr)
+library(cowplot)
+
+
+# load data
+load("MM_COMPASS_FM.Rdata")
+
+# only samples with gexp data
+fm <- fm[, !is.na(fm["N:GEXP:KRAS",])]
+
+# create df for plotting
+df <- as.data.frame(t(fm)) 
+
+# add subtypes
+subtypes <- rep("CCND1", length(fm))
+subtypes[fm["B:SAMP:cancermap_subtypes_WHSC1_FGFR3_Ig",]==1] <- "FGFR3"
+subtypes[fm["B:SAMP:cancermap_subtypes_Hyperdiploid",]==1] <- "Hyperdiploid/gain(11q)"
+subtypes[fm["B:SAMP:cancermap_subtypes_Hyperdiploid_amp1q",]==1] <- "Hyperdiploid/gain(1q)"
+subtypes[fm["B:SAMP:cancermap_subtypes_MAF_Ig",]==1] <- "MAF"
+subtypes[fm["B:SAMP:cancermap_subtypes_TRAF3_Aberrated",]==1] <- "TRAF3"
+subtypes[fm["B:SAMP:cancermap_cluster_CGA_Prolif",]==1] <- "CGA/Proliferative"
+ 
+df$subtype <- subtypes
+
+# function for boxplot of different subtypes
+subtype_bplot <- function(GEXP, ALT, TITLE, YLAB){
+  df <- df[,c(GEXP, ALT)] 
+  colnames(df) <- c("gexp", "alt") 
+  
+  ylabel <- gsub("N:GEXP:", "", gsub(":::::", "", GEXP))
+  
+  df <- df %>%
+    mutate(gexp = as.numeric(as.character(gexp))) %>%
+    mutate(alt = factor(alt, levels = sort(unique(alt))))
+  
+  ggplot(df, aes(x = alt, y = gexp, fill = alt)) +
+    geom_boxplot(outlier.shape = NA) +
+    geom_jitter(width = 0.2, color = "grey20") +
+    scale_fill_manual(values = brewer.pal(length(unique(df$alt)), "Set1")) +#,
+    ylab(YLAB) +
+    xlab("") +
+    ggtitle(TITLE) +
+    theme(legend.position="none",
+          axis.title = element_text(size = 16),
+          axis.text = element_text(size = 16),
+          axis.text.x = element_text(angle = 45, hjust = 1),
+          plot.title = element_text(size = 18, hjust = 0.5, face = "plain")) +
+    theme(plot.margin = unit(c(0.5,1,0,0), "cm"))
+}
+
+# plot number of CGAs in subtypes
+p <- subtype_bplot("N:SAMP:nCGA", "subtype", "CGAs expressed", "CGAs expressed")
+
+pdf("Figure6F_CoMMpass_CGA_subtype_boxplot.pdf", height = 6, width = 4)
+p
+dev.off()