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[8e0848]: / Fig5D_S5G_DLBCL_GSE98588_ligand_boxplots.R

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# Figure 5D and S5G oxplots of immunomodulatory ligand expression stratified by genetic alterations in DLBCL (GSE98588 Chapuy et al.)



library(ggpubr)

library(ggplot2)

library(RColorBrewer)

library(gridExtra)

library(dplyr)

library(cowplot)

library(readxl)





# load data

load("GSE98588_fm.Rdata")



# create matrix with selected genes

genes = as.character(read_excel("ligands.xlsx")$Gene)



feat <- paste0("N:GEXP:", paste0(genes, ":::::"))



rownames(fm)[grepl("6P", rownames(fm))]



df <- as.data.frame(t(fm)) 





# function for boxplot of altered vs unaltered cases

alt_bplot <- function(GEXP, ALT, TITLE){

  df <- df[,c(GEXP, ALT)] 

  colnames(df) <- c("gexp", "alt") 

  

  ylabel <- gsub("N:GEXP:", "", gsub(":::::", "", GEXP))

  

  alt_short <- gsub("([0-9])P([0-9])", "\\1p\\2", gsub("([0-9])Q([0-9])", "\\1q\\2", gsub("Q$", "q", gsub("P$", "p", gsub("B:.....", "", gsub("_", ".", gsub("SV_", "", gsub("_nonsynonymous:::::", "", gsub(":AMP", " amp ", gsub(":LOSS", " loss", gsub(":DEL", " del ", gsub(":SV", " SV  ", ALT))))))))))))

  alt_short <- ifelse(grepl("GNAB", ALT), paste0(alt_short, " mut "), alt_short)

  

  df <- df %>%

    mutate(gexp = as.numeric(as.character(gexp)),

           alt = gsub("^1", alt_short, 

                      gsub("^0", paste(gsub(".{5}$", "", alt_short), "WT "), alt))) %>%

    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 = 0.1, color = "grey20") +

    ylim(c(min(df$gexp)-(max(df$gexp)-min(df$gexp))*0.1, max(df$gexp)+(max(df$gexp)-min(df$gexp))*0.1)) +

    scale_fill_manual(values = brewer.pal(3, "Paired")[c(2,1)]) +

    ylab(substitute(italic(x)~" expression (log2)", list(x = ylabel))) +

    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)) +

    stat_compare_means(aes(label = ..p.signif..),

                       method = "wilcox.test",

                       method.args = list(alternative = "two.sided"),

                       comparisons = list(c(alt_short, paste(gsub(".{5}$", "", alt_short), "WT "))),

                       label.y = max(df$gexp)+(max(df$gexp)-min(df$gexp))*0.05

    ) +

    theme(plot.margin = unit(c(0.5,1,0,0), "cm"))

}



# plot selected alterations

p1 <- alt_bplot("N:GEXP:CD70", "B:GNAB:CD70", expression(paste(italic("CD70"))))

p2 <- alt_bplot("N:GEXP:MICB", "B:CNVR:6P21_33:LOSS", expression(paste(italic("MICB"))))



p6 <- alt_bplot("N:GEXP:TNFRSF14", "B:CNVR:BCL2:SV", expression(paste(italic("TNFRSF14"))))

p7 <- alt_bplot("N:GEXP:CD274", "B:CNVR:9P24_1:AMP", expression(paste(italic("CD274\n(PD-L1)"))))

p8 <- alt_bplot("N:GEXP:PDCD1LG2", "B:CNVR:9P24_1:AMP", expression(paste(italic("PDCD1LG2\n(PD-L2)"))))



pdf("Figure5D_DLBCL_GSE98588_CD70_boxplot.pdf", height = 5, width = 2)

p1 + scale_y_continuous(breaks = c(3,6,9,12), limits = c(2,12.5))

dev.off()



pdf("FigureS5G_DLBCL_GSE98588_MICB_TNFRSF14_CD274_PDCD1LG2_boxplot.pdf", height = 4, width = 10)

grid.arrange(p2, p6, p7, p8, ncol = 4)

dev.off()