--- a
+++ b/Fig1_plots.R
@@ -0,0 +1,70 @@
+GIT_HOME="/research/users/ppolonen/git_home/ImmunogenomicLandscape-BloodCancers/"
+source(file.path(GIT_HOME, "common_scripts/featurematrix/functions_generate_fm.R"))
+source(file.path(GIT_HOME, "common_scripts/visualisation/plotting_functions.R"))
+
+# Set working directory
+setwd("/research/groups/sysgen/PROJECTS/HEMAP_IMMUNOLOGY/petri_work/HEMAP_IMMUNOLOGY/Published_data_figures")
+
+# gexp data
+data=get(load("data9544_with_gene_symbols.RData"))
+
+# annotations
+annot = get(load("Hemap_immunology_Annotations.Rdata"))
+data=data[rownames(data)%in%annot[,1],]
+
+# make logical vectors
+annot$tbLY[annot$tbLY%in%c("Lymphoma_BCL_DLBCL_GCB", "Lymphoma_BCL_DLBCL_ABC")]="Lymphoma_BCL_DLBCL"
+tbly=get.logical(list(annot$tbLY), filterv = annot$CELLS_SORTED==0&!grepl("TCL", annot$tbLY)&!annot$CLASS2%in%"Cancer_Lymphoma_BCL_DLBCL_testicular")
+testicular=list("DLBCL_testicular"=annot$CLASS2%in%"Cancer_Lymphoma_BCL_DLBCL_testicular")
+tbly=tbly[sapply(tbly, sum)>5]
+
+tbly=append(tbly, testicular)
+
+lv=get.logical(list(annot$colorClass), filterv = annot$CELLS_SORTED==0&!grepl("TCL|T-ALL", annot$colorClass)&annot$Sample.type%in%c("Cancer", "Prolif"))
+names(lv)[3]="MDS"
+
+# barplots
+v=sapply(lv, function(lv2){
+  nr.high=sum(annot$CytolyticScore.1[lv2]=="high")
+  nr_samples=sum(lv2)
+  nr.high/nr_samples
+})
+v=sort(v, decreasing = T)
+v=signif(v*100,2)
+
+df2=data.frame(y=sort(v, decreasing = T), x=factor(names(v), levels = names(v)))
+
+# barplots Figure1:
+
+pdf("Fig1F.pdf",width = unit(4, "cm"),height = unit(3.5, "cm"))
+plot.boxplot("CytolyticScore", logicalVectors = lv, data = t(data.frame("CytolyticScore"=annot$CytolyticScore)), order.bl = T, intercept.y = 7.76, spread = F,outlier.size = 0.5,  color.v = c("#c08e94","#4ec173", "#f9c155", "#cd7bc1", "#266c34","#8a4bac"))
+dev.off()
+
+pdf("Fig1G.pdf", width = unit(3, "cm"),height = unit(2, "cm"))
+ggplot(data=df2, aes(x=x, y=v, fill=x)) +
+  geom_bar(stat="identity", position=position_dodge())+scale_fill_manual(values = c("#8a4bac", "#c08e94","#f9c155", "#266c34", "#4ec173",  "#cd7bc1"))+
+  geom_text(aes(label=df2$y), vjust=1.6, color="white",
+            position = position_dodge(0.9), size=3.5)+
+  theme_classic() +
+  theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust = 1))
+dev.off()
+
+# barplots
+v=sapply(tbly, function(lv2){
+  nr.high=sum(annot$CytolyticScore.1[lv2]=="high")
+  nr_samples=sum(lv2)
+  nr.high/nr_samples
+})
+v=sort(v, decreasing = T)
+
+names(v)=gsub("Lymphoma_BCL_", "", names(v))
+v=signif(v*100,2)
+df2=data.frame(y=sort(v, decreasing = T), x=factor(names(v), levels = names(v)))
+
+pdf("Fig1H.pdf", width = unit(3, "cm"),height = unit(2.5, "cm"))
+ggplot(data=df2, aes(x=x, y=y, fill="#c08e94")) +scale_fill_manual(values = c("#c08e94"))+
+  geom_bar(stat="identity", position=position_dodge())+
+  geom_text(aes(label=df2$y), vjust=1.6, color="white",
+            position = position_dodge(0.9), size=3.5)+
+  theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust = 1))
+dev.off()