Rscript

Makefile

@@ -22,7 +22,7 @@ all: ${TARGETS}
 	export PATH="${PBASE}/mamba/bin:${PATH}" && delly --version && touch .check
 
 download: .mamba .tools .rstats .pcks
-	export PATH="${PBASE}/mamba/bin:${PATH}" && cd data/ && gdown ${FILE} && tar -xzf sv.tar.gz && rm sv.tar.gz
+	export PATH="${PBASE}/mamba/bin:${PATH}" && cd data/ && gdown ${FILE} && tar -xzf sv.tar.gz && cp ${PBASE}/scripts/cnBafSV.R ${PBASE}/data/sv/ && rm sv.tar.gz
 
 clean:
 	rm -rf $(TARGETS) $(TARGETS:=.o) mamba/

scripts/cnBafSV.R

@@ -3,6 +3,8 @@ library(scales)
 library(gtable)
 library(grid)
 library(DNAcopy)
+library(gridExtra)
+library(cowplot)
 
 args = commandArgs(trailingOnly=TRUE)
 x = read.table(args[1], header=T)
@@ -21,7 +23,8 @@ if (length(args) == 1) { quit(); }
 # Read-depth + SVs
 sv = read.table(args[2], header=F)
 colnames(sv) = c("chr","start","end","type","id")
-p2 = p + geom_curve(data=sv, aes(x=start, xend=end, col=type), y=8, yend=8, curvature=-0.5)
+p2 = p
+if (length(args) <= 2) { p2 = p + geom_curve(data=sv, aes(x=start, xend=end, col=type), y=8, yend=8, curvature=-0.5); }
 p2 = p2 + labs(colour="SV type")
 seg=segments.summary(segment(smooth.CNA(CNA(log(x[,6]), rep("chr2", nrow(x)), x$start, data.type="logratio", sampleid="tumor")), undo.splits="sdundo", undo.SD=2))
 p3=p2 + geom_segment(data=seg, aes(x=loc.start, y=exp(seg.median), xend=loc.end, yend=exp(seg.median)), colour="darkorange")
@@ -39,9 +42,6 @@ q = q + scale_x_continuous(labels=comma)
 q = q + ylim(0,1)
 q = q + theme(axis.text.x = element_text(angle=45, hjust=1))
 p3 = p3 + xlim(min(baf$pos), max(baf$pos))
-g1 = ggplotGrob(p3)
-g2 = ggplotGrob(q)
-g = rbind(g1, g2, size="first")
-g$widths = unit.pmax(g1$widths, g2$widths)
-ggsave(g, file="cov.png", width=10, height=7)
+plot_grid(q, p3, align="v", nrow=2, rel_heights=c(1/3, 2/3))
+ggsave(file="cov.png", width=10, height=7)
 print(warnings())