62 lines
1.9 KiB
R
62 lines
1.9 KiB
R
source(paste(Sys.getenv("STING_DIR"), "/R/gsacommons.R", sep=""));
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args = commandArgs(TRUE);
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evalRoot = args[1];
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#if (is.na(evalRoot)) { evalRoot = "/home/radon01/kiran/scr1/projects/ESPGabrielDownsampling/results/v1/merged.vcf.eval120/eval"; }
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if (is.na(evalRoot)) { evalRoot = "/home/radon01/kiran/scr1/projects/ESPGabrielDownsampling/results/v1/merged.vcf.eval.v2/eval"; }
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plotRoot = args[2];
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if (is.na(plotRoot)) { plotRoot = "plot"; }
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eval = read.eval(evalRoot);
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# Venn diagram
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plot.begin(plotRoot, "venn");
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plot.callsetConcordance(eval);
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plot.end(plotRoot);
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# Venn by AC
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plot.begin(plotRoot, "venn_by_ac.all", width=12, height=8);
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plot.callsetConcordanceByAC(eval, novelty_name="all");
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plot.end(plotRoot);
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plot.begin(plotRoot, "venn_by_ac.known", width=12, height=8);
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plot.callsetConcordanceByAC(eval, novelty_name="known");
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plot.end(plotRoot);
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plot.begin(plotRoot, "venn_by_ac.novel", width=12, height=8);
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plot.callsetConcordanceByAC(eval, novelty_name="novel");
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plot.end(plotRoot);
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# Allele count spectrum
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plot.begin(plotRoot, "acs.all", width=12, height=8);
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plot.alleleCountSpectrum(eval, novelty_name="all");
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plot.end(plotRoot);
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plot.begin(plotRoot, "acs.known", width=12, height=8);
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plot.alleleCountSpectrum(eval, novelty_name="known");
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plot.end(plotRoot);
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plot.begin(plotRoot, "acs.novel", width=12, height=8);
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plot.alleleCountSpectrum(eval, novelty_name="novel");
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plot.end(plotRoot);
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# Ti/Tv spectrum
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plot.begin(plotRoot, "titv.all", width=12, height=8);
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plot.titvSpectrum(eval, novelty_name="all");
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plot.end(plotRoot);
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plot.begin(plotRoot, "titv.known", width=12, height=8);
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plot.titvSpectrum(eval, novelty_name="known");
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plot.end(plotRoot);
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plot.begin(plotRoot, "titv.novel", width=12, height=8);
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plot.titvSpectrum(eval, novelty_name="novel");
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plot.end(plotRoot);
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# Per-sample
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plot.begin(plotRoot, "variants_per_sample", width=12, height=8);
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plot.variantsPerSample(eval);
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plot.end(plotRoot);
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