“heatmap_hhb_version_2”

bin/make_heatmap.R

@@ -5,37 +5,71 @@ library("stringr")
 
 Args <- commandArgs()
 
-csv_data = fread(Args[6])
+correlation_file = Args[6]
 
-head(csv_data)
+p_file = Args[7]
 
-m_data <- melt(csv_data, id.vars=c("V1"))
+trait_name = fread(correlation_file)
 
-head(m_data)
+trait_name <- as.list(names(trait_name))
+trait_name <- trait_name[-1]
 
-pG = ggplot(m_data, aes(x = V1, y = variable, fill = value)) + geom_tile(color = "darkgrey") + scale_fill_stepsn(colors=c(low = "#075AFF",
+trait_name <- data.table(ID = trait_name)
+
+trait_name$ID <- sapply(trait_name$ID, toString)
+
+setkey(trait_name, "ID")
+
+Rho = fread(correlation_file)
+setkey(Rho, "V1")
+
+Pval = fread(p_file)
+setkey(Pval, "V1")
+
+Rho = Rho[trait_name$ID , c("V1",trait_name$ID), with=FALSE]
+Pval = Pval[trait_name$ID , c("V1",trait_name$ID), with=FALSE]
+
+cor_long = melt(as.data.table(Rho),id.vars=c('V1'))
+order_trait <- trait_name$ID
+
+pval_long =melt(as.data.table(Pval),id.vars=c('V1'))
+
+pval_long[,value := value*((dim(Rho)[1]-1)^2/2) ]
+ 
+pval_long[,pval_annote := c("***","**","*",".","")[.bincode(pval_long$value, c(-1, 0.001, 0.01, 0.05,0.1,1))]]
+ 
+pval_long[is.na(pval_long$pval_annote), pval_annote:=""]
+ 
+pval_long[,cor_val:= signif(round(cor_long$value, 2), 2)]
+ 
+pval_long[,full_annot := str_trim(paste0(cor_val, "\n",pval_annote))]
+
+pval_long$full_annot[pval_long$full_annot == "1"] <- ""
+
+cor_long[, variable:=ordered(cor_long$variable, levels=order_trait)]
+cor_long[, V1:=ordered(cor_long$V1, levels=order_trait)]
+
+pval_long[, variable:=ordered(pval_long$variable, levels=order_trait)]
+pval_long[, V1:=ordered(pval_long$V1, levels=order_trait)]
+
+pG = ggplot(cor_long, aes(x = V1, y = variable, fill = value)) + geom_tile(color = "darkgrey") + scale_fill_stepsn(colors=c(low = "#075AFF",
                         mid = "#FFFFCC",high = "#FF0000"), n.breaks=21, limits=c(-1,1), show.limits=T) 
+
+
 pG = pG + coord_fixed() + xlab("") + ylab("")+ theme_minimal()  + theme(axis.text = element_text(size=11), axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))
 pG = pG +  theme(legend.key.size = unit(1, 'cm'), #change legend key size
         legend.key.height = unit(2, 'cm'), #change legend key height
         legend.key.width = unit(1, 'cm'), #change legend key width
         legend.title = element_text(size=14), #change legend title font size
         legend.text = element_text(size=10))
-pG = pG + geom_text(data=m_data, aes(x=V1,y=variable,label=value), size=3.5)
 
+pG = pG + geom_text(data=pval_long, aes(x=V1,y=variable, label=full_annot), size=3.5)
 
 png(paste("HeatMap_", strsplit(Args[6], split=".", fixed=T)[[1]][1],".png", sep=""),width = 20, height    = 20,
   units     = "in",
   res       = 300,
   pointsize = 4)
-
 print(pG)
 dev.off()
 
 
-
- 
- 
-
- 
-

modules/LDSC.nf

@@ -116,10 +116,7 @@ process Make_HeatMap {
         params.compute_LDSC_matrix
 
     """
-        for matrix_csv in ${matrix_csv_files}
-        do
-            Rscript ${make_heatmap_script} \$matrix_csv
-        done
+        Rscript ${make_heatmap_script} Correlation_matrix_genetic.csv Pval_cor_matrix_genetic.csv
 
     """