From 8abba332ad5e9efb98b8e2054b4dc588aa54eff6 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Thu, 19 Oct 2017 23:43:17 -0400 Subject: [PATCH] replaced mapQ plot with sr roc figure legend and text to be updated later --- tex/bowtie2-s3.sam.eval | 28 +++++++++++++++++++ tex/bwa-s3.sam.eval | 52 ++++++++++++++++++++++++++++++++++ tex/mm2-s3.sam.eval | 60 +++++++++++++++++++++++++++++++++++++++ tex/mm2.eval | 26 ++++++----------- tex/roc.gp | 42 +++++++++++++++++----------- tex/snap-s3.sam.eval | 62 +++++++++++++++++++++++++++++++++++++++++ 6 files changed, 236 insertions(+), 34 deletions(-) create mode 100644 tex/bowtie2-s3.sam.eval create mode 100644 tex/bwa-s3.sam.eval create mode 100644 tex/mm2-s3.sam.eval create mode 100644 tex/snap-s3.sam.eval diff --git a/tex/bowtie2-s3.sam.eval b/tex/bowtie2-s3.sam.eval new file mode 100644 index 0000000..092247a --- /dev/null +++ b/tex/bowtie2-s3.sam.eval @@ -0,0 +1,28 @@ +Q 42 16872292 669 0.000039651 16872292 +Q 40 835329 636 0.000073697 17707621 +Q 31 6544 2 0.000073783 17714165 +Q 30 8882 6 0.000074084 17723047 +Q 27 68499 9 0.000074305 17791546 +Q 26 132041 81 0.000078277 17923587 +Q 25 129378 96 0.000083033 18052965 +Q 24 92056 382 0.000103665 18145021 +Q 23 14341 402 0.000125720 18159362 +Q 22 132838 146 0.000132789 18292200 +Q 21 122274 124 0.000138641 18414474 +Q 18 112183 103 0.000143361 18526657 +Q 17 126981 213 0.000153804 18653638 +Q 16 16356 208 0.000164810 18669994 +Q 15 42804 782 0.000206223 18712798 +Q 14 16026 318 0.000223025 18728824 +Q 12 170250 814 0.000264087 18899074 +Q 11 48351 1409 0.000337777 18947425 +Q 8 1843 311 0.000354156 18949268 +Q 7 62266 4435 0.000586276 19011534 +Q 6 413997 50057 0.003150647 19425531 +Q 5 404 58 0.003153568 19425935 +Q 4 704 154 0.003161381 19426639 +Q 3 1473 681 0.003196193 19428112 +Q 2 17541 16462 0.004039875 19445653 +Q 1 534344 354879 0.021693547 19979997 +Q 0 11939 9917 0.022176642 19991936 +U 8064 diff --git a/tex/bwa-s3.sam.eval b/tex/bwa-s3.sam.eval new file mode 100644 index 0000000..3aa9161 --- /dev/null +++ b/tex/bwa-s3.sam.eval @@ -0,0 +1,52 @@ +Q 60 18784147 3 0.000000160 18784147 +Q 52 19002 1 0.000000213 18803149 +Q 50 7152 2 0.000000319 18810301 +Q 49 6797 1 0.000000372 18817098 +Q 48 52188 2 0.000000477 18869286 +Q 47 48775 3 0.000000634 18918061 +Q 46 19447 2 0.000000739 18937508 +Q 45 25983 3 0.000000896 18963491 +Q 44 13455 1 0.000000949 18976946 +Q 43 14573 2 0.000001053 18991519 +Q 42 8697 4 0.000001263 19000216 +Q 41 8645 2 0.000001368 19008861 +Q 40 176603 75 0.000005264 19185464 +Q 38 2503 2 0.000005368 19187967 +Q 37 4117 3 0.000005523 19192084 +Q 36 2924 16 0.000006356 19195008 +Q 35 2323 8 0.000006772 19197331 +Q 34 2344 10 0.000007292 19199675 +Q 33 4279 6 0.000007603 19203954 +Q 32 2092 4 0.000007810 19206046 +Q 31 2625 11 0.000008382 19208671 +Q 30 2828 13 0.000009057 19211499 +Q 29 1581 1 0.000009108 19213080 +Q 28 1543 6 0.000009420 19214623 +Q 27 70916 223 0.000020948 19285539 +Q 26 1288 16 0.000021777 19286827 +Q 25 25551 122 0.000028065 19312378 +Q 24 14345 84 0.000032390 19326723 +Q 23 7308 87 0.000036878 19334031 +Q 22 8358 125 0.000043325 19342389 +Q 21 4836 71 0.000046983 19347225 +Q 20 5888 123 0.000053325 19353113 +Q 19 4656 83 0.000057600 19357769 +Q 18 3948 87 0.000062081 19361717 +Q 17 4418 114 0.000067954 19366135 +Q 16 4226 131 0.000074702 19370361 +Q 15 5760 164 0.000083144 19376121 +Q 14 4697 257 0.000096384 19380818 +Q 13 5246 313 0.000112503 19386064 +Q 12 4170 241 0.000124908 19390234 +Q 11 4095 304 0.000140557 19394329 +Q 10 3857 360 0.000159087 19398186 +Q 9 5300 438 0.000181617 19403486 +Q 8 4206 572 0.000211050 19407692 +Q 7 4676 787 0.000251541 19412368 +Q 6 3923 688 0.000286924 19416291 +Q 5 3294 708 0.000323333 19419585 +Q 4 2936 693 0.000358965 19422521 +Q 3 3928 816 0.000400897 19426449 +Q 2 2613 810 0.000442533 19429062 +Q 1 3515 1188 0.000503587 19432577 +Q 0 567423 376636 0.019321100 20000000 diff --git a/tex/mm2-s3.sam.eval b/tex/mm2-s3.sam.eval new file mode 100644 index 0000000..d4ea612 --- /dev/null +++ b/tex/mm2-s3.sam.eval @@ -0,0 +1,60 @@ +Q 60 18339260 12 0.000000654 18339260 +Q 59 51152 4 0.000000870 18390412 +Q 57 17831 2 0.000000978 18408243 +Q 56 48621 3 0.000001138 18456864 +Q 54 22767 4 0.000001353 18479631 +Q 53 19408 1 0.000001405 18499039 +Q 52 14488 4 0.000001620 18513527 +Q 51 13445 4 0.000001835 18526972 +Q 50 12408 2 0.000001942 18539380 +Q 49 11219 5 0.000002210 18550599 +Q 48 11333 3 0.000002370 18561932 +Q 47 16852 7 0.000002745 18578784 +Q 46 20284 8 0.000003172 18599068 +Q 45 16557 4 0.000003384 18615625 +Q 44 12134 7 0.000003758 18627759 +Q 43 25674 9 0.000004235 18653433 +Q 42 16752 15 0.000005035 18670185 +Q 41 13820 7 0.000005406 18684005 +Q 40 13195 10 0.000005937 18697200 +Q 39 12684 13 0.000006628 18709884 +Q 38 17095 9 0.000007102 18726979 +Q 37 17344 5 0.000007362 18744323 +Q 36 12333 9 0.000007837 18756656 +Q 35 12051 9 0.000008312 18768707 +Q 34 11978 12 0.000008945 18780685 +Q 33 12129 4 0.000009152 18792814 +Q 32 11703 14 0.000009891 18804517 +Q 31 11727 6 0.000010204 18816244 +Q 30 35149 31 0.000011829 18851393 +Q 29 11207 20 0.000012883 18862600 +Q 28 10842 23 0.000014094 18873442 +Q 27 15811 28 0.000015564 18889253 +Q 26 16984 39 0.000017613 18906237 +Q 25 13923 49 0.000020190 18920160 +Q 24 14244 44 0.000022499 18934404 +Q 23 13400 52 0.000025227 18947804 +Q 22 13198 39 0.000027266 18961002 +Q 21 13512 53 0.000030040 18974514 +Q 20 13462 55 0.000032916 18987976 +Q 19 13128 63 0.000036208 19001104 +Q 18 13418 50 0.000038812 19014522 +Q 17 13891 84 0.000043199 19028413 +Q 16 14196 86 0.000047683 19042609 +Q 15 14110 114 0.000053629 19056719 +Q 14 14769 150 0.000061453 19071488 +Q 13 17485 193 0.000071507 19088973 +Q 12 17466 259 0.000084998 19106439 +Q 11 17533 283 0.000099718 19123972 +Q 10 17783 312 0.000115925 19141755 +Q 9 18031 403 0.000136849 19159786 +Q 8 18268 489 0.000162217 19178054 +Q 7 19071 521 0.000189195 19197125 +Q 6 19904 655 0.000223083 19217029 +Q 5 19891 773 0.000263036 19236920 +Q 4 19956 1028 0.000316147 19256876 +Q 3 17141 1078 0.000371796 19274017 +Q 2 43396 6688 0.000717177 19317413 +Q 1 126848 25380 0.002017768 19444261 +Q 0 554003 371797 0.020553334 19998264 +U 1736 diff --git a/tex/mm2.eval b/tex/mm2.eval index 8f60797..2d0bed4 100644 --- a/tex/mm2.eval +++ b/tex/mm2.eval @@ -1,17 +1,9 @@ -Q 60 32072 0 0.000000000 -Q 43 206 1 0.000030981 -Q 27 201 1 0.000061578 -Q 15 59 1 0.000092200 -Q 12 25 1 0.000122839 -Q 11 16 1 0.000153473 -Q 10 24 1 0.000184032 -Q 9 17 2 0.000245248 -Q 8 27 3 0.000336938 -Q 7 23 1 0.000367309 -Q 6 20 1 0.000397675 -Q 5 18 4 0.000519751 -Q 4 17 1 0.000550038 -Q 3 29 5 0.000702204 -Q 2 32 4 0.000823522 -Q 1 54 6 0.001004872 -Q 0 234 106 0.004202697 +Q 60 32226 0 0.000000000 32226 +Q 20 266 1 0.000030777 32492 +Q 10 33 1 0.000061491 32525 +Q 9 120 1 0.000091898 32645 +Q 5 27 2 0.000153036 32672 +Q 4 68 2 0.000213806 32740 +Q 1 314 100 0.003237127 33054 +Q 0 31 17 0.003747922 33085 +U 3 diff --git a/tex/roc.gp b/tex/roc.gp index a053db8..9544bd2 100644 --- a/tex/roc.gp +++ b/tex/roc.gp @@ -14,7 +14,7 @@ set size 1.59,1.04 set multiplot layout 1,2 set label "(a)" at graph -0.245,1.06 font "Helvetica-bold,40" -set xlab "Error rate of mapped reads" +set xlab "Error rate of mapped PacBio reads" set ylab "Fraction of mapped reads" off +1.8 set ytics 0.02 set yran [0.9:1] @@ -34,19 +34,27 @@ unset label set origin 0.8,0 set size 0.79,1 set label "(b)" at graph -0.245,1.06 font "Helvetica-bold,40" -unset log -unset format -unset key -set log y -set ylab "Accumulative mapping error rate" off +0 -set xlab "Mapping quality" -set yran [1e-5:0.1] -set ytics 1e-5,0.1 -set format y "10^{%L}" -set xran [60:0] reverse -plot "<./eval2roc.pl blasr-mc.eval" u 1:2 w lp ls 4, \ - "<./eval2roc.pl bwa.eval" u 1:2 t "bwa-mem" w lp ls 2, \ - "<./eval2roc.pl graphmap.eval" u 1:2 t "graphmap" w lp ls 3, \ - "<./eval2roc.pl minialign.eval" u 1:2 t "minialign" w lp ls 1, \ - "<./eval2roc.pl mm2.eval" u 1:2 t "minimap2" w lp ls 6, \ - "<./eval2roc.pl ngmlr.eval" u 1:2 t "ngm-lr" w lp ls 5 +set xlab "Error rate of mapped short reads" + +set key top left +plot "<./eval2roc.pl -n2e7 bowtie2-s3.sam.eval" u 2:3 t "bowtie2" w lp ls 5, \ + "<./eval2roc.pl -n2e7 bwa-s3.sam.eval" u 2:3 t "bwa-mem" w lp ls 2, \ + "<./eval2roc.pl -n2e7 mm2-s3.sam.eval" u 2:3 t "minimap2" w lp ls 6, \ + "<./eval2roc.pl -n2e7 snap-s3.sam.eval" u 2:3 t "snap" w lp ls 3 + +#unset log +#unset format +#unset key +#set log y +#set ylab "Accumulative mapping error rate" off +0 +#set xlab "Mapping quality" +#set yran [1e-5:0.1] +#set ytics 1e-5,0.1 +#set format y "10^{%L}" +#set xran [60:0] reverse +#plot "<./eval2roc.pl blasr-mc.eval" u 1:2 w lp ls 4, \ +# "<./eval2roc.pl bwa.eval" u 1:2 t "bwa-mem" w lp ls 2, \ +# "<./eval2roc.pl graphmap.eval" u 1:2 t "graphmap" w lp ls 3, \ +# "<./eval2roc.pl minialign.eval" u 1:2 t "minialign" w lp ls 1, \ +# "<./eval2roc.pl mm2.eval" u 1:2 t "minimap2" w lp ls 6, \ +# "<./eval2roc.pl ngmlr.eval" u 1:2 t "ngm-lr" w lp ls 5 diff --git a/tex/snap-s3.sam.eval b/tex/snap-s3.sam.eval new file mode 100644 index 0000000..7988ba6 --- /dev/null +++ b/tex/snap-s3.sam.eval @@ -0,0 +1,62 @@ +Q 60 18993268 10320 0.000543350 18993268 +Q 59 33156 216 0.000553756 19026424 +Q 58 29982 295 0.000568365 19056406 +Q 57 9412 278 0.000582666 19065818 +Q 56 11012 228 0.000594281 19076830 +Q 55 9968 235 0.000606283 19086798 +Q 54 8602 292 0.000621301 19095400 +Q 53 6094 259 0.000634662 19101494 +Q 52 5026 257 0.000647946 19106520 +Q 51 4278 224 0.000659522 19110798 +Q 50 3682 178 0.000668708 19114480 +Q 49 2750 156 0.000676772 19117230 +Q 48 2314 112 0.000682548 19119544 +Q 47 2056 96 0.000687495 19121600 +Q 46 1658 62 0.000690677 19123258 +Q 45 1492 74 0.000694493 19124750 +Q 44 1150 56 0.000697379 19125900 +Q 43 1062 48 0.000699850 19126962 +Q 42 976 60 0.000702951 19127938 +Q 41 884 36 0.000704800 19128822 +Q 40 708 52 0.000707493 19129530 +Q 39 870 26 0.000708819 19130400 +Q 38 598 26 0.000710156 19130998 +Q 37 542 34 0.000711913 19131540 +Q 36 846 50 0.000714495 19132386 +Q 35 590 50 0.000717087 19132976 +Q 34 550 42 0.000719261 19133526 +Q 33 2174 66 0.000722628 19135700 +Q 32 876 86 0.000727089 19136576 +Q 31 638 104 0.000732500 19137214 +Q 30 1718 196 0.000742675 19138932 +Q 29 91022 968 0.000789497 19229954 +Q 28 12864 781 0.000829556 19242818 +Q 27 5806 427 0.000851489 19248624 +Q 26 25274 728 0.000888144 19273898 +Q 25 7418 680 0.000923070 19281316 +Q 24 11800 701 0.000958839 19293116 +Q 23 57328 3933 0.001159250 19350444 +Q 22 7662 846 0.001202494 19358106 +Q 21 5924 617 0.001233989 19364030 +Q 20 4623 574 0.001263330 19368653 +Q 19 4988 942 0.001311627 19373641 +Q 18 3968 793 0.001352282 19377609 +Q 17 3630 681 0.001387166 19381239 +Q 16 2921 513 0.001413422 19384160 +Q 15 2716 424 0.001435095 19386876 +Q 14 2366 365 0.001453744 19389242 +Q 13 2169 412 0.001474828 19391411 +Q 12 2077 360 0.001493233 19393488 +Q 11 2016 441 0.001515815 19395504 +Q 10 2292 738 0.001553682 19397796 +Q 9 4165 1832 0.001647772 19401961 +Q 8 3963 1862 0.001743385 19405924 +Q 7 3927 1793 0.001835408 19409851 +Q 6 3572 1639 0.001919497 19413423 +Q 5 3270 1533 0.001998126 19416693 +Q 4 3046 1610 0.002080718 19419739 +Q 3 251447 125550 0.008436553 19671186 +Q 2 24390 13537 0.009113417 19695576 +Q 1 124406 86780 0.013434624 19819982 +Q 0 171254 153874 0.021016609 19991236 +U 8764