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results: small changes to generating plots
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178 changes: 106 additions & 72 deletions
178
results/kmer_size_experiment/results/generate-results.sh
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,120 +1,154 @@ | ||
| #!/bin/bash | ||
| set -eou pipefail | ||
| set -x | ||
|
|
||
| # Set to 1 to filter out k=99, else include k99 | ||
| HIDE_K99=0 | ||
|
|
||
| if (($HIDE_K99)); then | ||
| OUTDIR=latest_k91 | ||
| else | ||
| OUTDIR=latest_k99 | ||
| fi | ||
|
|
||
| mkdir -p $OUTDIR | ||
|
|
||
| # hide k99 files | ||
| echo "-- hiding k=99" | ||
| for d in perfect_cov stoch_cov stocherr_cov stocherr_corr | ||
| do | ||
| if [ -d ../$d/k99 ] | ||
| then | ||
| mv ../$d/k99 ../$d/hidden_k99 | ||
| fi | ||
| done | ||
| if (($HIDE_K99)); then | ||
| echo "-- hiding k=99" | ||
| for d in perfect_cov stoch_cov stocherr_cov stocherr_corr | ||
| do | ||
| if [ -d ../$d/k99 ] | ||
| then | ||
| mv ../$d/k99 ../$d/hidden_k99 | ||
| fi | ||
| done | ||
| fi | ||
|
|
||
| mkdir -p latest | ||
| echo "-- Perfect Coverage" | ||
| ./make-csv.sh ../perfect_cov/k*/stats.plain.txt > latest/perfect.plain.csv | ||
| ./make-csv.sh ../perfect_cov/k*/stats.links.txt > latest/perfect.links.csv | ||
| ./make-csv.sh ../perfect_cov/k*/stats.pe.txt > latest/perfect.pe.csv | ||
| ./plot-ng50-and-errs.R "Perfect cov. (100X, 100bp reads)" latest/perfect.pdf \ | ||
| latest/perfect.plain.csv latest/perfect.links.csv latest/perfect.pe.csv | ||
| ./make-csv.sh ../perfect_cov/k*/stats.plain.txt > $OUTDIR/perfect.plain.csv | ||
| ./make-csv.sh ../perfect_cov/k*/stats.links.txt > $OUTDIR/perfect.links.csv | ||
| ./make-csv.sh ../perfect_cov/k*/stats.pe.txt > $OUTDIR/perfect.pe.csv | ||
| ./plot-ng50-and-errs.R "Perfect cov. (100X, 100bp reads)" $OUTDIR/perfect.pdf \ | ||
| $OUTDIR/perfect.plain.csv $OUTDIR/perfect.links.csv $OUTDIR/perfect.pe.csv | ||
|
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| ./plot-ng50-and-errs.R "Perfect cov. (100X, 100bp reads)" latest/perfect_no_pe.pdf \ | ||
| latest/perfect.plain.csv latest/perfect.links.csv | ||
| ./plot-ng50-and-errs.R "Perfect cov. (100X, 100bp reads)" $OUTDIR/perfect_no_pe.pdf \ | ||
| $OUTDIR/perfect.plain.csv $OUTDIR/perfect.links.csv | ||
|
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||
| echo "-- Stochastic Coverage" | ||
| ./make-csv.sh ../stoch_cov/k*/stats.plain.txt > latest/stoch.plain.csv | ||
| ./make-csv.sh ../stoch_cov/k*/stats.links.txt > latest/stoch.links.csv | ||
| ./make-csv.sh ../stoch_cov/k*/stats.pe.txt > latest/stoch.pe.csv | ||
| ./plot-ng50-and-errs.R "Stochastic cov. (100X, 100bp reads)" latest/stoch.pdf \ | ||
| latest/stoch.plain.csv latest/stoch.links.csv latest/stoch.pe.csv | ||
| ./make-csv.sh ../stoch_cov/k*/stats.plain.txt > $OUTDIR/stoch.plain.csv | ||
| ./make-csv.sh ../stoch_cov/k*/stats.links.txt > $OUTDIR/stoch.links.csv | ||
| ./make-csv.sh ../stoch_cov/k*/stats.pe.txt > $OUTDIR/stoch.pe.csv | ||
| ./plot-ng50-and-errs.R "Stochastic cov. (100X, 100bp reads)" $OUTDIR/stoch.pdf \ | ||
| $OUTDIR/stoch.plain.csv $OUTDIR/stoch.links.csv $OUTDIR/stoch.pe.csv | ||
|
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| echo "-- Stochastic Coverage + Error" | ||
| ./make-csv.sh ../stocherr_cov/k*/stats.plain.txt > latest/stocherr.plain.csv | ||
| ./make-csv.sh ../stocherr_cov/k*/stats.links.txt > latest/stocherr.links.csv | ||
| ./make-csv.sh ../stocherr_cov/k*/stats.pe.txt > latest/stocherr.pe.csv | ||
| ./plot-ng50-and-errs.R "Stochastic cov. + 0.5% err (100X, 100bp reads)" latest/stocherr.pdf \ | ||
| latest/stocherr.plain.csv latest/stocherr.links.csv latest/stocherr.pe.csv | ||
| ./make-csv.sh ../stocherr_cov/k*/stats.plain.txt > $OUTDIR/stocherr.plain.csv | ||
| ./make-csv.sh ../stocherr_cov/k*/stats.links.txt > $OUTDIR/stocherr.links.csv | ||
| ./make-csv.sh ../stocherr_cov/k*/stats.pe.txt > $OUTDIR/stocherr.pe.csv | ||
| ./plot-ng50-and-errs.R "Stochastic cov. + 0.5% err (100X, 100bp reads)" $OUTDIR/stocherr.pdf \ | ||
| $OUTDIR/stocherr.plain.csv $OUTDIR/stocherr.links.csv $OUTDIR/stocherr.pe.csv | ||
|
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| echo "-- Stochastic Coverage + Error + Error Correction" | ||
| ./make-csv.sh ../stocherr_corr/k*/stats.plain.txt > latest/stocherrcorr.plain.csv | ||
| ./make-csv.sh ../stocherr_corr/k*/stats.links.txt > latest/stocherrcorr.links.csv | ||
| ./make-csv.sh ../stocherr_corr/k*/stats.pe.txt > latest/stocherrcorr.pe.csv | ||
| ./plot-ng50-and-errs.R "Stochastic cov. + 0.5% err + correct (100X, 100bp reads)" latest/stocherrcorr.pdf \ | ||
| latest/stocherr.plain.csv latest/stocherr.links.csv latest/stocherr.pe.csv \ | ||
| latest/stocherrcorr.plain.csv latest/stocherrcorr.links.csv latest/stocherrcorr.pe.csv | ||
| ./make-csv.sh ../stocherr_corr/k*/stats.plain.txt > $OUTDIR/stocherrcorr.plain.csv | ||
| ./make-csv.sh ../stocherr_corr/k*/stats.links.txt > $OUTDIR/stocherrcorr.links.csv | ||
| ./make-csv.sh ../stocherr_corr/k*/stats.pe.txt > $OUTDIR/stocherrcorr.pe.csv | ||
| ./plot-ng50-and-errs.R "Stochastic cov. + 0.5% err + correct (100X, 100bp reads)" $OUTDIR/stocherrcorr.pdf \ | ||
| $OUTDIR/stocherr.plain.csv $OUTDIR/stocherr.links.csv $OUTDIR/stocherr.pe.csv \ | ||
| $OUTDIR/stocherrcorr.plain.csv $OUTDIR/stocherrcorr.links.csv $OUTDIR/stocherrcorr.pe.csv | ||
|
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| # Gather SGA results | ||
| if [ -d ../stocherr_cov/sga ] | ||
| then | ||
| echo "-- SGA plots" | ||
| # ../stocherr_cov/sga/k21/stats.k21.txt | ||
| ./make-csv.sh ../stocherr_cov/sga/k*/stats.k*.txt > latest/stocherr.sga.csv | ||
| ./plot-mccortex-vs-sga.R latest/links-vs-sga-ng50.pdf latest/links-vs-sga-errs.pdf latest/stocherr.links.csv latest/stocherr.sga.csv | ||
| ./plot-mccortex-vs-sga.R latest/pe-vs-sga-ng50.pdf latest/pe-vs-sga-errs.pdf latest/stocherr.pe.csv latest/stocherr.sga.csv | ||
| ./make-csv.sh ../stocherr_cov/sga/k*/stats.k*.txt > $OUTDIR/stocherr.sga.csv | ||
| ./plot-mccortex-vs-sga.R $OUTDIR/links-vs-sga-ng50.pdf $OUTDIR/links-vs-sga-errs.pdf $OUTDIR/stocherr.links.csv $OUTDIR/stocherr.sga.csv | ||
| ./plot-mccortex-vs-sga.R $OUTDIR/pe-vs-sga-ng50.pdf $OUTDIR/pe-vs-sga-errs.pdf $OUTDIR/stocherr.pe.csv $OUTDIR/stocherr.sga.csv | ||
| fi | ||
|
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| if [ -d ../stocherr_corr/sga ] | ||
| then | ||
| echo "-- SGA + Error Correction plots" | ||
| # ../stocherr_corr/sga/k21/stats.k21.txt | ||
| ./make-csv.sh ../stocherr_corr/sga/k*/stats.k*.txt > latest/stocherrcorr.sga.csv | ||
| ./plot-mccortex-vs-sga.R latest/corr-links-vs-sga-ng50.pdf latest/corr-links-vs-sga-errs.pdf latest/stocherrcorr.links.csv latest/stocherrcorr.sga.csv | ||
| ./plot-mccortex-vs-sga.R latest/corr-pe-vs-sga-ng50.pdf latest/corr-pe-vs-sga-errs.pdf latest/stocherrcorr.pe.csv latest/stocherrcorr.sga.csv | ||
| ./make-csv.sh ../stocherr_corr/sga/k*/stats.k*.txt > $OUTDIR/stocherrcorr.sga.csv | ||
| ./plot-mccortex-vs-sga.R $OUTDIR/corr-links-vs-sga-ng50.pdf $OUTDIR/corr-links-vs-sga-errs.pdf $OUTDIR/stocherrcorr.links.csv $OUTDIR/stocherrcorr.sga.csv | ||
| ./plot-mccortex-vs-sga.R $OUTDIR/corr-pe-vs-sga-ng50.pdf $OUTDIR/corr-pe-vs-sga-errs.pdf $OUTDIR/stocherrcorr.pe.csv $OUTDIR/stocherrcorr.sga.csv | ||
| # McCortex (SE) vs McCortex (PE) vs SGA (all with bfc corrected reads) | ||
| ./plot-mccortex-se-pe-vs-sga.R $OUTDIR/corr-both-vs-sga-ng50.pdf $OUTDIR/corr-both-vs-sga-errs.pdf $OUTDIR/stocherrcorr.links.csv $OUTDIR/stocherrcorr.pe.csv $OUTDIR/stocherrcorr.sga.csv | ||
| # McCortex (SE) vs McCortex (PE) vs SGA (not with bfc corrected reads) | ||
| ./plot-mccortex-se-pe-vs-sga.R $OUTDIR/both-vs-sga-ng50.pdf $OUTDIR/both-vs-sga-errs.pdf $OUTDIR/stocherr.links.csv $OUTDIR/stocherr.pe.csv $OUTDIR/stocherr.sga.csv | ||
| # Corrected + McCortex vs raw + SGA | ||
| ./plot-mccortex-vs-sga.R latest/corr-links-vs-raw-sga-ng50.pdf latest/corr-links-vs-raw-sga-errs.pdf latest/stocherrcorr.links.csv latest/stocherr.sga.csv | ||
| ./plot-mccortex-vs-sga.R latest/corr-pe-vs-raw-sga-ng50.pdf latest/corr-pe-vs-raw-sga-errs.pdf latest/stocherrcorr.pe.csv latest/stocherr.sga.csv | ||
| ./plot-mccortex-vs-sga.R $OUTDIR/corr-links-vs-raw-sga-ng50.pdf $OUTDIR/corr-links-vs-raw-sga-errs.pdf $OUTDIR/stocherrcorr.links.csv $OUTDIR/stocherr.sga.csv | ||
| ./plot-mccortex-vs-sga.R $OUTDIR/corr-pe-vs-raw-sga-ng50.pdf $OUTDIR/corr-pe-vs-raw-sga-errs.pdf $OUTDIR/stocherrcorr.pe.csv $OUTDIR/stocherr.sga.csv | ||
| fi | ||
|
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||
| echo "-- Plain vs links" | ||
| ./plot-ng50-three-sets.R latest/plain-vs-links.pdf \ | ||
| latest/perfect.plain.csv latest/perfect.links.csv \ | ||
| latest/stoch.plain.csv latest/stoch.links.csv \ | ||
| latest/stocherr.plain.csv latest/stocherr.links.csv | ||
| ./plot-ng50-three-sets.R $OUTDIR/plain-vs-links-ng50.pdf $OUTDIR/plain-vs-links-errs.pdf \ | ||
| $OUTDIR/perfect.plain.csv $OUTDIR/perfect.links.csv \ | ||
| $OUTDIR/stoch.plain.csv $OUTDIR/stoch.links.csv \ | ||
| $OUTDIR/stocherr.plain.csv $OUTDIR/stocherr.links.csv | ||
|
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| echo "-- Plain vs PE" | ||
| ./plot-ng50-three-sets.R latest/plain-vs-pe.pdf \ | ||
| latest/perfect.plain.csv latest/perfect.pe.csv \ | ||
| latest/stoch.plain.csv latest/stoch.pe.csv \ | ||
| latest/stocherr.plain.csv latest/stocherr.pe.csv | ||
| ./plot-ng50-three-sets.R $OUTDIR/plain-vs-pe-ng50.pdf $OUTDIR/plain-vs-pe-errs.pdf \ | ||
| $OUTDIR/perfect.plain.csv $OUTDIR/perfect.pe.csv \ | ||
| $OUTDIR/stoch.plain.csv $OUTDIR/stoch.pe.csv \ | ||
| $OUTDIR/stocherr.plain.csv $OUTDIR/stocherr.pe.csv | ||
|
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| echo "-- Plain vs links (with error correction)" | ||
| ./plot-ng50-three-sets.R latest/plain-vs-links-corr.pdf \ | ||
| latest/perfect.plain.csv latest/perfect.links.csv \ | ||
| latest/stoch.plain.csv latest/stoch.links.csv \ | ||
| latest/stocherrcorr.plain.csv latest/stocherrcorr.links.csv | ||
| ./plot-ng50-three-sets.R $OUTDIR/plain-vs-links-corr-ng50.pdf $OUTDIR/plain-vs-links-corr-errs.pdf \ | ||
| $OUTDIR/perfect.plain.csv $OUTDIR/perfect.links.csv \ | ||
| $OUTDIR/stoch.plain.csv $OUTDIR/stoch.links.csv \ | ||
| $OUTDIR/stocherrcorr.plain.csv $OUTDIR/stocherrcorr.links.csv | ||
|
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| echo "-- Plain vs PE links (with error correction)" | ||
| ./plot-ng50-three-sets.R latest/plain-vs-pe-corr.pdf \ | ||
| latest/perfect.plain.csv latest/perfect.pe.csv \ | ||
| latest/stoch.plain.csv latest/stoch.pe.csv \ | ||
| latest/stocherrcorr.plain.csv latest/stocherrcorr.pe.csv | ||
| ./plot-ng50-three-sets.R $OUTDIR/plain-vs-pe-corr-ng50.pdf $OUTDIR/plain-vs-pe-corr-errs.pdf \ | ||
| $OUTDIR/perfect.plain.csv $OUTDIR/perfect.pe.csv \ | ||
| $OUTDIR/stoch.plain.csv $OUTDIR/stoch.pe.csv \ | ||
| $OUTDIR/stocherrcorr.plain.csv $OUTDIR/stocherrcorr.pe.csv | ||
|
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| echo "-- Plain vs links (perfect, stochastic, error, corrected)" | ||
| ./plot-ng50-four-sets.R $OUTDIR/plain-vs-links-fourway-ng50.pdf $OUTDIR/plain-vs-links-fourway-errs.pdf \ | ||
| $OUTDIR/perfect.plain.csv $OUTDIR/perfect.links.csv \ | ||
| $OUTDIR/stoch.plain.csv $OUTDIR/stoch.links.csv \ | ||
| $OUTDIR/stocherr.plain.csv $OUTDIR/stocherr.links.csv \ | ||
| $OUTDIR/stocherrcorr.plain.csv $OUTDIR/stocherrcorr.links.csv | ||
|
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| echo "-- Plain vs PE (perfect, stochastic, error, corrected)" | ||
| ./plot-ng50-four-sets.R $OUTDIR/plain-vs-pe-fourway-ng50.pdf $OUTDIR/plain-vs-pe-fourway-errs.pdf \ | ||
| $OUTDIR/perfect.plain.csv $OUTDIR/perfect.pe.csv \ | ||
| $OUTDIR/stoch.plain.csv $OUTDIR/stoch.pe.csv \ | ||
| $OUTDIR/stocherr.plain.csv $OUTDIR/stocherr.pe.csv \ | ||
| $OUTDIR/stocherrcorr.plain.csv $OUTDIR/stocherrcorr.pe.csv | ||
|
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| echo "-- Making cleaning tables" | ||
| ./make-cleaning-table.py ../stocherr_cov/k*/graph.k*.dist.txt > latest/cleaning.table.csv | ||
| ./make-cleaning-table.py ../stocherr_corr/k*/graph.k*.dist.txt > latest/cleaning.corr.table.csv | ||
| ./make-cleaning-table.py ../stocherr_cov/k*/graph.k*.dist.txt > $OUTDIR/cleaning.table.csv | ||
| ./make-cleaning-table.py ../stocherr_corr/k*/graph.k*.dist.txt > $OUTDIR/cleaning.corr.table.csv | ||
|
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| echo "-- Make link count csv" | ||
| for t in se pe; do | ||
| cat ../perfect_cov/k*/graph.k*.$t.raw.ctp.gz.log | ./count-links.pl > latest/perfect.linkcounts.$t.csv | ||
| cat ../stoch_cov/k*/graph.k*.$t.raw.ctp.gz.log | ./count-links.pl > latest/stoch.linkcounts.$t.csv | ||
| cat ../stocherr_cov/k*/graph.k*.$t.raw.ctp.gz.log | ./count-links.pl > latest/stocherr.linkcounts.$t.csv | ||
| cat ../stocherr_corr/k*/graph.k*.$t.raw.ctp.gz.log | ./count-links.pl > latest/stocherrcorr.linkcounts.$t.csv | ||
| cat ../perfect_cov/k*/graph.k*.$t.raw.ctp.gz.log | ./count-links.pl > $OUTDIR/perfect.linkcounts.$t.csv | ||
| cat ../stoch_cov/k*/graph.k*.$t.raw.ctp.gz.log | ./count-links.pl > $OUTDIR/stoch.linkcounts.$t.csv | ||
| cat ../stocherr_cov/k*/graph.k*.$t.raw.ctp.gz.log | ./count-links.pl > $OUTDIR/stocherr.linkcounts.$t.csv | ||
| cat ../stocherr_corr/k*/graph.k*.$t.raw.ctp.gz.log | ./count-links.pl > $OUTDIR/stocherrcorr.linkcounts.$t.csv | ||
| done | ||
| for t in se pe; do | ||
| for s in perfect stoch stocherr stocherrcorr; do | ||
| ./plot-link-counts.R latest/$s.linkcounts.$t.pdf latest/$s.linkcounts.$t.csv | ||
| ./plot-link-counts.R "$OUTDIR/$s"_linkcounts_$t.pdf $OUTDIR/$s.linkcounts.$t.csv | ||
| done | ||
| ./plot-link-counts-together.R latest/linkcounts.$t.pdf latest/{perfect,stoch,stocherr,stocherrcorr}.linkcounts.$t.csv | ||
| ./plot-link-counts-threeway.R $OUTDIR/linkcounts_$t\_threeway.pdf $OUTDIR/{perfect,stoch,stocherr}.linkcounts.$t.csv | ||
| ./plot-link-counts-together.R $OUTDIR/linkcounts_$t\_fourway.pdf $OUTDIR/{perfect,stoch,stocherr,stocherrcorr}.linkcounts.$t.csv | ||
| done | ||
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| # unhide k99 files | ||
| echo "-- recovering k=99" | ||
| for d in perfect_cov stoch_cov stocherr_cov stocherr_corr | ||
| do | ||
| if [ -d ../$d/hidden_k99 ] | ||
| then | ||
| mv ../$d/hidden_k99 ../$d/k99 | ||
| fi | ||
| done | ||
| if (($HIDE_K99)); then | ||
| echo "-- recovering k=99" | ||
| for d in perfect_cov stoch_cov stocherr_cov stocherr_corr | ||
| do | ||
| if [ -d ../$d/hidden_k99 ] | ||
| then | ||
| mv ../$d/hidden_k99 ../$d/k99 | ||
| fi | ||
| done | ||
| fi |
62 changes: 62 additions & 0 deletions
62
results/kmer_size_experiment/results/plot-link-counts-threeway.R
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,62 @@ | ||
| #!/usr/bin/env Rscript --vanilla | ||
|
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| # Isaac Turner 2017-02-16 | ||
|
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| args <- commandArgs(trailingOnly=TRUE) | ||
| if(length(args) != 4) { | ||
| stop("Usage: ./plot-link-counts.R <linkcounts.pdf> <perfect.csv> <stoch.csv> <stocherr.csv>\n") | ||
| } | ||
|
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|
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| plot_path <- "latest/linkcounts.se.pdf" | ||
| perf_path <- "latest/perfect.linkcounts.se.csv" | ||
| stoch_path <- "latest/stoch.linkcounts.se.csv" | ||
| error_path <- "latest/stocherr.linkcounts.se.csv" | ||
|
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| plot_path = args[1] | ||
| perf_path <- args[2] | ||
| stoch_path <- args[3] | ||
| error_path <- args[4] | ||
|
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| a <- read.table(perf_path, sep='\t',head=T,comment.char='#',as.is=T) | ||
| b <- read.table(stoch_path, sep='\t',head=T,comment.char='#',as.is=T) | ||
| c <- read.table(error_path, sep='\t',head=T,comment.char='#',as.is=T) | ||
|
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| nlinkkmers_ylim <- ceiling(max(a$n_link_kmers, b$n_link_kmers, c$n_link_kmers)) | ||
| kmers <- a$K | ||
|
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| # * joins with no spaces, ~ joins with a space | ||
| xlabel = expression(italic('k')) | ||
| ylabel = expression('no. of '*italic('k')*'mers with links (log)') | ||
|
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| pdf(plot_path, width=6, height=6) | ||
|
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| # Remove empty title space | ||
| par(mar=c(4,5,2,2)+0.1) # set margins: bottom, left, top and right | ||
| par(xpd=TRUE) | ||
|
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| legend_labels <- c("perfect", "stochastic", "error") | ||
| cols <- c('#1b9e77', '#d95f02', '#7570b3') # from color brewer | ||
| pnts <- c(19,4,17) # point styles pch= | ||
| jf <- 0.2 # jitter factor | ||
| lt <- 2 # line thickness | ||
|
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| plot(1, type='n', bty="n", xlab='', ylab='', log='y', | ||
| xlim=c(20,100), ylim=c(1,nlinkkmers_ylim), axes=F) | ||
|
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| points(jitter(a$K,jf), a$n_link_kmers, type='b', lwd=lt, pch=pnts[1], col=cols[1], lty=1) | ||
| points(jitter(b$K,jf), b$n_link_kmers, type='b', lwd=lt, pch=pnts[2], col=cols[2], lty=1) | ||
| points(jitter(c$K,jf), c$n_link_kmers, type='b', lwd=lt, pch=pnts[3], col=cols[3], lty=1) | ||
|
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| mtext(side=1, text=xlabel, line=2) | ||
| mtext(side=2, text=ylabel, line=4) | ||
| axis(1, at=a$K) | ||
| axis(2, las=2) | ||
|
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| par(xpd=TRUE) | ||
| legend("topright", bty="n", inset=c(0.2,0), | ||
| legend=legend_labels, | ||
| col=cols, lwd=lt, lty=c(1,1,1), | ||
| pch=pnts) | ||
|
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| dev.off() |
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