Merge branch 'main' of github.com:tobiasrausch/vc

tobiasrausch · Jun 26, 2024 · b6fcb1a · b6fcb1a
2 parents 75ca1cd + 970b0e8
commit b6fcb1a
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diff --git a/Makefile b/Makefile
@@ -10,19 +10,19 @@ all: ${TARGETS}
 	curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-$(shell uname)-$(shell uname -m).sh" && bash Mambaforge-$(shell uname)-$(shell uname -m).sh -b -p mamba && rm "Mambaforge-$(shell uname)-$(shell uname -m).sh" && touch .mamba
 
 .tools: .mamba
-	export PATH=${PBASE}/mamba/bin:${PATH} && mamba install -y -c conda-forge -c bioconda datamash samtools bcftools bedtools htslib bwa delly alfred freebayes igv wally minimap2 && touch .tools
+	export PATH="${PBASE}/mamba/bin:${PATH}" && mamba install -y -c conda-forge -c bioconda datamash samtools bcftools bedtools htslib bwa delly alfred freebayes igv wally minimap2 && touch .tools
 
 .rstats: .mamba .tools
-	export PATH=${PBASE}/mamba/bin:${PATH} && mamba install -y -c conda-forge -c bioconda bioconductor-genomicfeatures r-ggplot2 r-reshape2 r-gridextra r-cowplot bioconductor-dnacopy && touch .rstats
+	export PATH="${PBASE}/mamba/bin:${PATH}" && mamba install -y -c conda-forge -c bioconda bioconductor-genomicfeatures r-ggplot2 r-reshape2 r-gridextra r-cowplot bioconductor-dnacopy && touch .rstats
 
 .pcks: .mamba .tools .rstats
-	export PATH=${PBASE}/mamba/bin:${PATH} && mamba install -y -c conda-forge -c bioconda cyvcf2 numpy pysam && pip install gdown && touch .pcks
+	export PATH="${PBASE}/mamba/bin:${PATH}" && mamba install -y -c conda-forge -c bioconda cyvcf2 numpy pysam && pip install gdown && touch .pcks
 
 .check: .mamba .tools .rstats .pcks
-	export PATH=${PBASE}/mamba/bin:${PATH} && delly --version && touch .check
+	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/
diff --git a/README.md b/README.md
@@ -20,17 +20,6 @@ Download the course data:
 
 `make FILE=1nxzjQFt33ch1P_nWF66q1tkHv5gxTaKb download`
 
-## Installation - Mac OS
-
-Load the conda environment with all required tools
-
-`conda env create -f environment.yml`
-
-Download and unpack the course data
-
-`cd data/ && gdown 1nxzjQFt33ch1P_nWF66q1tkHv5gxTaKb && tar -xzf sv.tar.gz && rm sv.tar.gz`
-
-
 ## Load the software stack
 
 Load the mamba environment with all required tools

diff --git a/scripts/cnBafSV.R b/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())