Integrate plot-clustering.R in snakemake pipeline

Snakefile

@@ -349,6 +349,20 @@ rule generate_halo_json:
         "(./utils/counts_to_json.py {input.counts} | gzip > {output.json}) 2> {log}"
 
 
+
+rule plot_clustering:
+    input:
+        sv_calls  = "sv_calls/{sample}/{windows}.{bpdens}/{method}.txt",
+        binbed = "utils/bin_200kb_all.bed",
+    output:
+        position = "sv_calls/{sample}/{windows}.{bpdens,selected_j[0-9\\.]+_s[0-9\\.]+}/plots/sv_clustering/{method}-position.pdf",
+        chromosome = "sv_calls/{sample}/{windows}.{bpdens,selected_j[0-9\\.]+_s[0-9\\.]+}/plots/sv_clustering/{method}-chromosome.pdf",
+    log:
+        "log/plot_clustering/{sample}/{windows}.{bpdens}.{method}.log"
+    script:
+        "utils/plot-clustering.snakemake.R"
+
+
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utils/plot-clustering.snakemake.R

+log <- file(snakemake@log[[1]], open='wt')
+sink(file=log, type='message')
+sink(file=log, type='output')
+
+source("utils/plot-clustering.R")
+plot.clustering(inputfile = snakemake@input[["sv_calls"]], bin.bed.filename = snakemake@input[["binbed"]], position.outputfile = snakemake@output[["position"]], chromosome.outputfile = snakemake@output[["chromosome"]])