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results: small changes to generating plots
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‎results/kmer_size_experiment/Makefile‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -19,8 +19,8 @@ GENREADS=$(CTXDIR)/scripts/python/generate-reads.py
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COUNT_BAD_EDGES=python $(CTXDIR)/scripts/python/count-bad-edges.py
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TIME=/usr/bin/time -l
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22-
# REF=$(CTXDIR)/results/data/chr22/chr22_17M_18M.fa
23-
REF=$(CTXDIR)/results/data/chr22/chr22_28M_29M.fa
22+
REF=$(CTXDIR)/results/data/chr22/chr22_17M_18M.fa
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# REF=$(CTXDIR)/results/data/chr22/chr22_28M_29M.fa
2424
PERFECT=data/perfect_cov
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STOCH=data/stoch_cov
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STOCHERR=data/stocherr_cov

‎results/kmer_size_experiment/notes.txt‎

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@@ -5,6 +5,9 @@ generated if you have it installed (e.g. with `brew install science/sga`).
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Specify the absolue path to the reference FASTA:
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REF=../data/chr22/chr22_28M_29M.fa
8+
# OR
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REF=../data/chr22/chr22_17M_18M.fa
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# Then convert to absolute path
811
REF=$(cd "$(dirname "$REF")"; pwd)/$(basename "$REF")
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Sample reads and assemble with:

‎results/kmer_size_experiment/results/generate-results.sh‎

Lines changed: 106 additions & 72 deletions
Original file line numberDiff line numberDiff line change
@@ -1,120 +1,154 @@
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#!/bin/bash
22
set -eou pipefail
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set -x
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# Set to 1 to filter out k=99, else include k99
6+
HIDE_K99=0
7+
8+
if (($HIDE_K99)); then
9+
OUTDIR=latest_k91
10+
else
11+
OUTDIR=latest_k99
12+
fi
13+
14+
mkdir -p $OUTDIR
315

416
# hide k99 files
5-
echo "-- hiding k=99"
6-
for d in perfect_cov stoch_cov stocherr_cov stocherr_corr
7-
do
8-
if [ -d ../$d/k99 ]
9-
then
10-
mv ../$d/k99 ../$d/hidden_k99
11-
fi
12-
done
17+
if (($HIDE_K99)); then
18+
echo "-- hiding k=99"
19+
for d in perfect_cov stoch_cov stocherr_cov stocherr_corr
20+
do
21+
if [ -d ../$d/k99 ]
22+
then
23+
mv ../$d/k99 ../$d/hidden_k99
24+
fi
25+
done
26+
fi
1327

14-
mkdir -p latest
1528
echo "-- Perfect Coverage"
16-
./make-csv.sh ../perfect_cov/k*/stats.plain.txt > latest/perfect.plain.csv
17-
./make-csv.sh ../perfect_cov/k*/stats.links.txt > latest/perfect.links.csv
18-
./make-csv.sh ../perfect_cov/k*/stats.pe.txt > latest/perfect.pe.csv
19-
./plot-ng50-and-errs.R "Perfect cov. (100X, 100bp reads)" latest/perfect.pdf \
20-
latest/perfect.plain.csv latest/perfect.links.csv latest/perfect.pe.csv
29+
./make-csv.sh ../perfect_cov/k*/stats.plain.txt > $OUTDIR/perfect.plain.csv
30+
./make-csv.sh ../perfect_cov/k*/stats.links.txt > $OUTDIR/perfect.links.csv
31+
./make-csv.sh ../perfect_cov/k*/stats.pe.txt > $OUTDIR/perfect.pe.csv
32+
./plot-ng50-and-errs.R "Perfect cov. (100X, 100bp reads)" $OUTDIR/perfect.pdf \
33+
$OUTDIR/perfect.plain.csv $OUTDIR/perfect.links.csv $OUTDIR/perfect.pe.csv
2134

22-
./plot-ng50-and-errs.R "Perfect cov. (100X, 100bp reads)" latest/perfect_no_pe.pdf \
23-
latest/perfect.plain.csv latest/perfect.links.csv
35+
./plot-ng50-and-errs.R "Perfect cov. (100X, 100bp reads)" $OUTDIR/perfect_no_pe.pdf \
36+
$OUTDIR/perfect.plain.csv $OUTDIR/perfect.links.csv
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2538
echo "-- Stochastic Coverage"
26-
./make-csv.sh ../stoch_cov/k*/stats.plain.txt > latest/stoch.plain.csv
27-
./make-csv.sh ../stoch_cov/k*/stats.links.txt > latest/stoch.links.csv
28-
./make-csv.sh ../stoch_cov/k*/stats.pe.txt > latest/stoch.pe.csv
29-
./plot-ng50-and-errs.R "Stochastic cov. (100X, 100bp reads)" latest/stoch.pdf \
30-
latest/stoch.plain.csv latest/stoch.links.csv latest/stoch.pe.csv
39+
./make-csv.sh ../stoch_cov/k*/stats.plain.txt > $OUTDIR/stoch.plain.csv
40+
./make-csv.sh ../stoch_cov/k*/stats.links.txt > $OUTDIR/stoch.links.csv
41+
./make-csv.sh ../stoch_cov/k*/stats.pe.txt > $OUTDIR/stoch.pe.csv
42+
./plot-ng50-and-errs.R "Stochastic cov. (100X, 100bp reads)" $OUTDIR/stoch.pdf \
43+
$OUTDIR/stoch.plain.csv $OUTDIR/stoch.links.csv $OUTDIR/stoch.pe.csv
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3245
echo "-- Stochastic Coverage + Error"
33-
./make-csv.sh ../stocherr_cov/k*/stats.plain.txt > latest/stocherr.plain.csv
34-
./make-csv.sh ../stocherr_cov/k*/stats.links.txt > latest/stocherr.links.csv
35-
./make-csv.sh ../stocherr_cov/k*/stats.pe.txt > latest/stocherr.pe.csv
36-
./plot-ng50-and-errs.R "Stochastic cov. + 0.5% err (100X, 100bp reads)" latest/stocherr.pdf \
37-
latest/stocherr.plain.csv latest/stocherr.links.csv latest/stocherr.pe.csv
46+
./make-csv.sh ../stocherr_cov/k*/stats.plain.txt > $OUTDIR/stocherr.plain.csv
47+
./make-csv.sh ../stocherr_cov/k*/stats.links.txt > $OUTDIR/stocherr.links.csv
48+
./make-csv.sh ../stocherr_cov/k*/stats.pe.txt > $OUTDIR/stocherr.pe.csv
49+
./plot-ng50-and-errs.R "Stochastic cov. + 0.5% err (100X, 100bp reads)" $OUTDIR/stocherr.pdf \
50+
$OUTDIR/stocherr.plain.csv $OUTDIR/stocherr.links.csv $OUTDIR/stocherr.pe.csv
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3952
echo "-- Stochastic Coverage + Error + Error Correction"
40-
./make-csv.sh ../stocherr_corr/k*/stats.plain.txt > latest/stocherrcorr.plain.csv
41-
./make-csv.sh ../stocherr_corr/k*/stats.links.txt > latest/stocherrcorr.links.csv
42-
./make-csv.sh ../stocherr_corr/k*/stats.pe.txt > latest/stocherrcorr.pe.csv
43-
./plot-ng50-and-errs.R "Stochastic cov. + 0.5% err + correct (100X, 100bp reads)" latest/stocherrcorr.pdf \
44-
latest/stocherr.plain.csv latest/stocherr.links.csv latest/stocherr.pe.csv \
45-
latest/stocherrcorr.plain.csv latest/stocherrcorr.links.csv latest/stocherrcorr.pe.csv
53+
./make-csv.sh ../stocherr_corr/k*/stats.plain.txt > $OUTDIR/stocherrcorr.plain.csv
54+
./make-csv.sh ../stocherr_corr/k*/stats.links.txt > $OUTDIR/stocherrcorr.links.csv
55+
./make-csv.sh ../stocherr_corr/k*/stats.pe.txt > $OUTDIR/stocherrcorr.pe.csv
56+
./plot-ng50-and-errs.R "Stochastic cov. + 0.5% err + correct (100X, 100bp reads)" $OUTDIR/stocherrcorr.pdf \
57+
$OUTDIR/stocherr.plain.csv $OUTDIR/stocherr.links.csv $OUTDIR/stocherr.pe.csv \
58+
$OUTDIR/stocherrcorr.plain.csv $OUTDIR/stocherrcorr.links.csv $OUTDIR/stocherrcorr.pe.csv
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4760
# Gather SGA results
4861
if [ -d ../stocherr_cov/sga ]
4962
then
5063
echo "-- SGA plots"
5164
# ../stocherr_cov/sga/k21/stats.k21.txt
52-
./make-csv.sh ../stocherr_cov/sga/k*/stats.k*.txt > latest/stocherr.sga.csv
53-
./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
54-
./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
65+
./make-csv.sh ../stocherr_cov/sga/k*/stats.k*.txt > $OUTDIR/stocherr.sga.csv
66+
./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
67+
./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
5568
fi
5669

5770
if [ -d ../stocherr_corr/sga ]
5871
then
5972
echo "-- SGA + Error Correction plots"
6073
# ../stocherr_corr/sga/k21/stats.k21.txt
61-
./make-csv.sh ../stocherr_corr/sga/k*/stats.k*.txt > latest/stocherrcorr.sga.csv
62-
./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
63-
./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
74+
./make-csv.sh ../stocherr_corr/sga/k*/stats.k*.txt > $OUTDIR/stocherrcorr.sga.csv
75+
./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
76+
./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
77+
# McCortex (SE) vs McCortex (PE) vs SGA (all with bfc corrected reads)
78+
./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
79+
# McCortex (SE) vs McCortex (PE) vs SGA (not with bfc corrected reads)
80+
./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
6481
# Corrected + McCortex vs raw + SGA
65-
./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
66-
./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
82+
./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
83+
./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
6784
fi
6885

6986
echo "-- Plain vs links"
70-
./plot-ng50-three-sets.R latest/plain-vs-links.pdf \
71-
latest/perfect.plain.csv latest/perfect.links.csv \
72-
latest/stoch.plain.csv latest/stoch.links.csv \
73-
latest/stocherr.plain.csv latest/stocherr.links.csv
87+
./plot-ng50-three-sets.R $OUTDIR/plain-vs-links-ng50.pdf $OUTDIR/plain-vs-links-errs.pdf \
88+
$OUTDIR/perfect.plain.csv $OUTDIR/perfect.links.csv \
89+
$OUTDIR/stoch.plain.csv $OUTDIR/stoch.links.csv \
90+
$OUTDIR/stocherr.plain.csv $OUTDIR/stocherr.links.csv
7491

7592
echo "-- Plain vs PE"
76-
./plot-ng50-three-sets.R latest/plain-vs-pe.pdf \
77-
latest/perfect.plain.csv latest/perfect.pe.csv \
78-
latest/stoch.plain.csv latest/stoch.pe.csv \
79-
latest/stocherr.plain.csv latest/stocherr.pe.csv
93+
./plot-ng50-three-sets.R $OUTDIR/plain-vs-pe-ng50.pdf $OUTDIR/plain-vs-pe-errs.pdf \
94+
$OUTDIR/perfect.plain.csv $OUTDIR/perfect.pe.csv \
95+
$OUTDIR/stoch.plain.csv $OUTDIR/stoch.pe.csv \
96+
$OUTDIR/stocherr.plain.csv $OUTDIR/stocherr.pe.csv
8097

8198
echo "-- Plain vs links (with error correction)"
82-
./plot-ng50-three-sets.R latest/plain-vs-links-corr.pdf \
83-
latest/perfect.plain.csv latest/perfect.links.csv \
84-
latest/stoch.plain.csv latest/stoch.links.csv \
85-
latest/stocherrcorr.plain.csv latest/stocherrcorr.links.csv
99+
./plot-ng50-three-sets.R $OUTDIR/plain-vs-links-corr-ng50.pdf $OUTDIR/plain-vs-links-corr-errs.pdf \
100+
$OUTDIR/perfect.plain.csv $OUTDIR/perfect.links.csv \
101+
$OUTDIR/stoch.plain.csv $OUTDIR/stoch.links.csv \
102+
$OUTDIR/stocherrcorr.plain.csv $OUTDIR/stocherrcorr.links.csv
86103

87104
echo "-- Plain vs PE links (with error correction)"
88-
./plot-ng50-three-sets.R latest/plain-vs-pe-corr.pdf \
89-
latest/perfect.plain.csv latest/perfect.pe.csv \
90-
latest/stoch.plain.csv latest/stoch.pe.csv \
91-
latest/stocherrcorr.plain.csv latest/stocherrcorr.pe.csv
105+
./plot-ng50-three-sets.R $OUTDIR/plain-vs-pe-corr-ng50.pdf $OUTDIR/plain-vs-pe-corr-errs.pdf \
106+
$OUTDIR/perfect.plain.csv $OUTDIR/perfect.pe.csv \
107+
$OUTDIR/stoch.plain.csv $OUTDIR/stoch.pe.csv \
108+
$OUTDIR/stocherrcorr.plain.csv $OUTDIR/stocherrcorr.pe.csv
109+
110+
echo "-- Plain vs links (perfect, stochastic, error, corrected)"
111+
./plot-ng50-four-sets.R $OUTDIR/plain-vs-links-fourway-ng50.pdf $OUTDIR/plain-vs-links-fourway-errs.pdf \
112+
$OUTDIR/perfect.plain.csv $OUTDIR/perfect.links.csv \
113+
$OUTDIR/stoch.plain.csv $OUTDIR/stoch.links.csv \
114+
$OUTDIR/stocherr.plain.csv $OUTDIR/stocherr.links.csv \
115+
$OUTDIR/stocherrcorr.plain.csv $OUTDIR/stocherrcorr.links.csv
116+
117+
echo "-- Plain vs PE (perfect, stochastic, error, corrected)"
118+
./plot-ng50-four-sets.R $OUTDIR/plain-vs-pe-fourway-ng50.pdf $OUTDIR/plain-vs-pe-fourway-errs.pdf \
119+
$OUTDIR/perfect.plain.csv $OUTDIR/perfect.pe.csv \
120+
$OUTDIR/stoch.plain.csv $OUTDIR/stoch.pe.csv \
121+
$OUTDIR/stocherr.plain.csv $OUTDIR/stocherr.pe.csv \
122+
$OUTDIR/stocherrcorr.plain.csv $OUTDIR/stocherrcorr.pe.csv
92123

93124
echo "-- Making cleaning tables"
94-
./make-cleaning-table.py ../stocherr_cov/k*/graph.k*.dist.txt > latest/cleaning.table.csv
95-
./make-cleaning-table.py ../stocherr_corr/k*/graph.k*.dist.txt > latest/cleaning.corr.table.csv
125+
./make-cleaning-table.py ../stocherr_cov/k*/graph.k*.dist.txt > $OUTDIR/cleaning.table.csv
126+
./make-cleaning-table.py ../stocherr_corr/k*/graph.k*.dist.txt > $OUTDIR/cleaning.corr.table.csv
96127

97128
echo "-- Make link count csv"
98129
for t in se pe; do
99-
cat ../perfect_cov/k*/graph.k*.$t.raw.ctp.gz.log | ./count-links.pl > latest/perfect.linkcounts.$t.csv
100-
cat ../stoch_cov/k*/graph.k*.$t.raw.ctp.gz.log | ./count-links.pl > latest/stoch.linkcounts.$t.csv
101-
cat ../stocherr_cov/k*/graph.k*.$t.raw.ctp.gz.log | ./count-links.pl > latest/stocherr.linkcounts.$t.csv
102-
cat ../stocherr_corr/k*/graph.k*.$t.raw.ctp.gz.log | ./count-links.pl > latest/stocherrcorr.linkcounts.$t.csv
130+
cat ../perfect_cov/k*/graph.k*.$t.raw.ctp.gz.log | ./count-links.pl > $OUTDIR/perfect.linkcounts.$t.csv
131+
cat ../stoch_cov/k*/graph.k*.$t.raw.ctp.gz.log | ./count-links.pl > $OUTDIR/stoch.linkcounts.$t.csv
132+
cat ../stocherr_cov/k*/graph.k*.$t.raw.ctp.gz.log | ./count-links.pl > $OUTDIR/stocherr.linkcounts.$t.csv
133+
cat ../stocherr_corr/k*/graph.k*.$t.raw.ctp.gz.log | ./count-links.pl > $OUTDIR/stocherrcorr.linkcounts.$t.csv
103134
done
104135
for t in se pe; do
105136
for s in perfect stoch stocherr stocherrcorr; do
106-
./plot-link-counts.R latest/$s.linkcounts.$t.pdf latest/$s.linkcounts.$t.csv
137+
./plot-link-counts.R "$OUTDIR/$s"_linkcounts_$t.pdf $OUTDIR/$s.linkcounts.$t.csv
107138
done
108-
./plot-link-counts-together.R latest/linkcounts.$t.pdf latest/{perfect,stoch,stocherr,stocherrcorr}.linkcounts.$t.csv
139+
./plot-link-counts-threeway.R $OUTDIR/linkcounts_$t\_threeway.pdf $OUTDIR/{perfect,stoch,stocherr}.linkcounts.$t.csv
140+
./plot-link-counts-together.R $OUTDIR/linkcounts_$t\_fourway.pdf $OUTDIR/{perfect,stoch,stocherr,stocherrcorr}.linkcounts.$t.csv
109141
done
110142

111143

112144
# unhide k99 files
113-
echo "-- recovering k=99"
114-
for d in perfect_cov stoch_cov stocherr_cov stocherr_corr
115-
do
116-
if [ -d ../$d/hidden_k99 ]
117-
then
118-
mv ../$d/hidden_k99 ../$d/k99
119-
fi
120-
done
145+
if (($HIDE_K99)); then
146+
echo "-- recovering k=99"
147+
for d in perfect_cov stoch_cov stocherr_cov stocherr_corr
148+
do
149+
if [ -d ../$d/hidden_k99 ]
150+
then
151+
mv ../$d/hidden_k99 ../$d/k99
152+
fi
153+
done
154+
fi

‎results/kmer_size_experiment/results/plot-link-counts-threeway.R‎

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#!/usr/bin/env Rscript --vanilla
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3+
# Isaac Turner 2017-02-16
4+
5+
args <- commandArgs(trailingOnly=TRUE)
6+
if(length(args) != 4) {
7+
stop("Usage: ./plot-link-counts.R <linkcounts.pdf> <perfect.csv> <stoch.csv> <stocherr.csv>\n")
8+
}
9+
10+
11+
plot_path <- "latest/linkcounts.se.pdf"
12+
perf_path <- "latest/perfect.linkcounts.se.csv"
13+
stoch_path <- "latest/stoch.linkcounts.se.csv"
14+
error_path <- "latest/stocherr.linkcounts.se.csv"
15+
16+
plot_path = args[1]
17+
perf_path <- args[2]
18+
stoch_path <- args[3]
19+
error_path <- args[4]
20+
21+
a <- read.table(perf_path, sep='\t',head=T,comment.char='#',as.is=T)
22+
b <- read.table(stoch_path, sep='\t',head=T,comment.char='#',as.is=T)
23+
c <- read.table(error_path, sep='\t',head=T,comment.char='#',as.is=T)
24+
25+
nlinkkmers_ylim <- ceiling(max(a$n_link_kmers, b$n_link_kmers, c$n_link_kmers))
26+
kmers <- a$K
27+
28+
# * joins with no spaces, ~ joins with a space
29+
xlabel = expression(italic('k'))
30+
ylabel = expression('no. of '*italic('k')*'mers with links (log)')
31+
32+
pdf(plot_path, width=6, height=6)
33+
34+
# Remove empty title space
35+
par(mar=c(4,5,2,2)+0.1) # set margins: bottom, left, top and right
36+
par(xpd=TRUE)
37+
38+
legend_labels <- c("perfect", "stochastic", "error")
39+
cols <- c('#1b9e77', '#d95f02', '#7570b3') # from color brewer
40+
pnts <- c(19,4,17) # point styles pch=
41+
jf <- 0.2 # jitter factor
42+
lt <- 2 # line thickness
43+
44+
plot(1, type='n', bty="n", xlab='', ylab='', log='y',
45+
xlim=c(20,100), ylim=c(1,nlinkkmers_ylim), axes=F)
46+
47+
points(jitter(a$K,jf), a$n_link_kmers, type='b', lwd=lt, pch=pnts[1], col=cols[1], lty=1)
48+
points(jitter(b$K,jf), b$n_link_kmers, type='b', lwd=lt, pch=pnts[2], col=cols[2], lty=1)
49+
points(jitter(c$K,jf), c$n_link_kmers, type='b', lwd=lt, pch=pnts[3], col=cols[3], lty=1)
50+
51+
mtext(side=1, text=xlabel, line=2)
52+
mtext(side=2, text=ylabel, line=4)
53+
axis(1, at=a$K)
54+
axis(2, las=2)
55+
56+
par(xpd=TRUE)
57+
legend("topright", bty="n", inset=c(0.2,0),
58+
legend=legend_labels,
59+
col=cols, lwd=lt, lty=c(1,1,1),
60+
pch=pnts)
61+
62+
dev.off()

‎results/kmer_size_experiment/results/plot-mccortex-vs-sga.R‎

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -76,7 +76,8 @@ plot(1, type='n', bty="n", log="y", axes=F,
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points(jitter(a$K,jf), a$AssemblyErrors+1, type='b', lwd=lt, pch=pnts[3], col=cols[3], lty=1)
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points(jitter(b$K,jf), b$AssemblyErrors+1, type='b', lwd=lt, pch=pnts[4], col=cols[4], lty=1)
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axis(1, at=kmers)
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axis(2, at=c(1,2,11,51,101,201,501), labels=c(0,1,10,50,100,200,500), las=2)
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axis(2, at=c(1,2,11,51,101,201,501,1001,2001,4001),
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labels=c(0,1,10,50,100,200,500,1000,2000,4000), las=2)
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par(xpd=TRUE)
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legend("topright", bty="n", inset=c(0.2,-0.15),

‎results/kmer_size_experiment/results/plot-ng50-and-errs.R‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -107,7 +107,7 @@ N50_ylim <- 100
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asm_ylim <- 5
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if(use_pe) {
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N50_ylim <- 150
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asm_ylim <- 1000
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asm_ylim <- 2000
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}
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xlabel = expression(italic('k'))

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