├── .gitignore ├── LICENSE ├── README.md ├── example ├── draw.sh ├── test1.paf ├── test1.paf.png ├── test2.paf └── test2.paf.png └── paf2dotplot.r /.gitignore: -------------------------------------------------------------------------------- 1 | # History files 2 | .Rhistory 3 | .Rapp.history 4 | 5 | # Session Data files 6 | .RData 7 | 8 | # User-specific files 9 | .Ruserdata 10 | 11 | # Example code in package build process 12 | *-Ex.R 13 | 14 | # Output files from R CMD build 15 | /*.tar.gz 16 | 17 | # Output files from R CMD check 18 | /*.Rcheck/ 19 | 20 | # RStudio files 21 | .Rproj.user/ 22 | 23 | # produced vignettes 24 | vignettes/*.html 25 | vignettes/*.pdf 26 | 27 | # OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3 28 | .httr-oauth 29 | 30 | # knitr and R markdown default cache directories 31 | *_cache/ 32 | /cache/ 33 | 34 | # Temporary files created by R markdown 35 | *.utf8.md 36 | *.knit.md 37 | 38 | # R Environment Variables 39 | .Renviron 40 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | GNU GENERAL PUBLIC LICENSE 2 | Version 3, 29 June 2007 3 | 4 | Copyright (C) 2007 Free Software Foundation, Inc. 5 | Everyone is permitted to copy and distribute verbatim copies 6 | of this license document, but changing it is not allowed. 7 | 8 | Preamble 9 | 10 | The GNU General Public License is a free, copyleft license for 11 | software and other kinds of works. 12 | 13 | The licenses for most software and other practical works are designed 14 | to take away your freedom to share and change the works. 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Interpretation of Sections 15 and 16. 613 | 614 | If the disclaimer of warranty and limitation of liability provided 615 | above cannot be given local legal effect according to their terms, 616 | reviewing courts shall apply local law that most closely approximates 617 | an absolute waiver of all civil liability in connection with the 618 | Program, unless a warranty or assumption of liability accompanies a 619 | copy of the Program in return for a fee. 620 | 621 | END OF TERMS AND CONDITIONS 622 | 623 | How to Apply These Terms to Your New Programs 624 | 625 | If you develop a new program, and you want it to be of the greatest 626 | possible use to the public, the best way to achieve this is to make it 627 | free software which everyone can redistribute and change under these terms. 628 | 629 | To do so, attach the following notices to the program. It is safest 630 | to attach them to the start of each source file to most effectively 631 | state the exclusion of warranty; and each file should have at least 632 | the "copyright" line and a pointer to where the full notice is found. 633 | 634 | 635 | Copyright (C) 636 | 637 | This program is free software: you can redistribute it and/or modify 638 | it under the terms of the GNU General Public License as published by 639 | the Free Software Foundation, either version 3 of the License, or 640 | (at your option) any later version. 641 | 642 | This program is distributed in the hope that it will be useful, 643 | but WITHOUT ANY WARRANTY; without even the implied warranty of 644 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 645 | GNU General Public License for more details. 646 | 647 | You should have received a copy of the GNU General Public License 648 | along with this program. If not, see . 649 | 650 | Also add information on how to contact you by electronic and paper mail. 651 | 652 | If the program does terminal interaction, make it output a short 653 | notice like this when it starts in an interactive mode: 654 | 655 | Copyright (C) 656 | This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. 657 | This is free software, and you are welcome to redistribute it 658 | under certain conditions; type `show c' for details. 659 | 660 | The hypothetical commands `show w' and `show c' should show the appropriate 661 | parts of the General Public License. Of course, your program's commands 662 | might be different; for a GUI interface, you would use an "about box". 663 | 664 | You should also get your employer (if you work as a programmer) or school, 665 | if any, to sign a "copyright disclaimer" for the program, if necessary. 666 | For more information on this, and how to apply and follow the GNU GPL, see 667 | . 668 | 669 | The GNU General Public License does not permit incorporating your program 670 | into proprietary programs. If your program is a subroutine library, you 671 | may consider it more useful to permit linking proprietary applications with 672 | the library. If this is what you want to do, use the GNU Lesser General 673 | Public License instead of this License. But first, please read 674 | . 675 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # Paf2dotplot 2 | Draw a dot plot from a paf alignment (usually generated by [minimap2](https://github.com/lh3/minimap2)). Paf2dotplot is adapted from [dotPlotly](https://github.com/tpoorten/dotPlotly/), but it has some extra features and parameters, for details, just have a try! 3 | 4 | ## Dependencies 5 | The script requires two R packages: `optparse`, `ggplot2` 6 | 7 | ## Installation 8 | ```sh 9 | # download 10 | git clone https://github.com/moold/paf2dotplot.git 11 | # install R packages 12 | R --slave -e 'install.packages(c("optparse", "ggplot2"))' 13 | ``` 14 | 15 | ## Usage 16 | ```sh 17 | # do asm-to-ref mapping 18 | minimap2 -cx asm10 asm1.fa asm2.fa > aln.paf 19 | # draw 20 | ./paf2dotplot.r -f -b aln.paf 21 | ``` 22 | This will generate a result file `aln.paf.pdf` in the current directory. You can use [ImageMagick](https://github.com/ImageMagick/ImageMagick) command to do some format conversion or modification. 23 | Here are two example images generated by Paf2dotplot: 24 | ![1-to-many](./example/test1.paf.png) ![many-to-many](./example/test2.paf.png) 25 | 26 | ## Parameters 27 | Use `./paf2dotplot.r -h` to see options. 28 | 29 | 30 | 31 | 32 | 33 | -------------------------------------------------------------------------------- /example/draw.sh: -------------------------------------------------------------------------------- 1 | ../paf2dotplot.r -f -b --plot-size 10 test1.paf 2 | ../paf2dotplot.r -f -s --plot-size 10 test2.paf 3 | -------------------------------------------------------------------------------- /example/test1.paf: -------------------------------------------------------------------------------- 1 | ctg88l 1768524 1548099 1763622 - chr1 248387328 2717 216558 206277 222337 60 2 | ctg88l 1768524 1042011 1548007 - chr1 248387328 216657 717448 499797 506714 60 3 | ctg88l 1768524 345993 1041882 - chr1 248387328 717595 1414140 691464 700000 60 4 | ctg88l 1768524 203194 344101 - chr1 248387328 1416751 1556779 139729 140948 60 5 | ctg88l 1768524 45028 201722 - chr1 248387328 1558979 1716291 156406 157435 60 6 | ctg10l 50517107 50357073 50517105 - chr1 248387328 1764476 1924872 159500 160667 60 7 | ctg10l 50517107 50168138 50357040 - chr1 248387328 1924862 2111552 185899 189387 60 8 | ctg10l 50517107 49899281 50040072 - chr1 248387328 2198276 2223285 24312 141403 55 9 | ctg10l 50517107 49774743 49869939 - chr1 248387328 2251429 2359976 94831 108788 60 10 | ctg10l 50517107 49450315 49774044 - chr1 248387328 2360358 2684348 321994 325279 60 11 | ctg10l 50517107 48559492 49449312 - chr1 248387328 2684689 3576299 885895 894394 60 12 | ctg10l 50517107 47988599 48523424 - chr1 248387328 3611507 4146302 533392 535322 60 13 | ctg10l 50517107 46603928 47987471 - chr1 248387328 4147024 5530883 1380838 1385083 60 14 | ctg10l 50517107 45867181 46603713 - chr1 248387328 5531616 6268417 735703 737208 60 15 | ctg10l 50517107 45667027 45866651 - chr1 248387328 6269025 6468889 199306 200045 60 16 | ctg10l 50517107 45107885 45666684 - chr1 248387328 6469547 7028815 558016 559501 60 17 | ctg10l 50517107 44103186 45087733 - chr1 248387328 7050544 8035199 982451 985909 60 18 | ctg10l 50517107 42409262 44103077 - chr1 248387328 8035335 9730687 1691579 1696559 60 19 | ctg10l 50517107 39515240 42408081 - chr1 248387328 9731823 12623062 2883329 2898087 60 20 | ctg10l 50517107 39294044 39496898 - chr1 248387328 12641412 12768723 124133 205257 60 21 | ctg10l 50517107 38441506 39187704 - chr1 248387328 12804313 13551984 745072 748034 60 22 | ctg10l 50517107 38037356 38440728 - chr1 248387328 13554615 13957970 402549 403625 60 23 | ctg10l 50517107 37304873 38037241 - chr1 248387328 13958155 14690812 731402 732963 60 24 | ctg10l 50517107 36509398 37304849 - chr1 248387328 14690840 15473650 781562 795895 60 25 | ctg10l 50517107 35920465 36508691 - chr1 248387328 15474336 16081337 586838 607556 60 26 | ctg10l 50517107 35329821 35773910 - chr1 248387328 16152845 16626283 435272 480115 60 27 | ctg10l 50517107 33450473 35220207 - chr1 248387328 16557899 18322914 1760903 1771471 60 28 | ctg10l 50517107 32921911 33450290 - chr1 248387328 18323048 18850633 526834 528614 60 29 | ctg10l 50517107 31236623 32921602 - chr1 248387328 18850930 20538770 1682437 1688913 60 30 | ctg10l 50517107 30769241 31236352 - chr1 248387328 20539394 21006465 466342 467578 60 31 | ctg10l 50517107 30574025 30769014 - chr1 248387328 21006772 21201577 194651 195046 60 32 | ctg10l 50517107 29937164 30573899 - chr1 248387328 21201727 21835333 631937 637483 60 33 | ctg10l 50517107 26937173 29936462 - chr1 248387328 21836067 24837955 2995122 3003941 60 34 | ctg10l 50517107 25537636 26936887 - chr1 248387328 24838333 26237471 1397125 1400189 60 35 | ctg10l 50517107 22379860 25537327 - chr1 248387328 26237906 29395022 3153783 3159137 60 36 | ctg10l 50517107 21525415 22379046 - chr1 248387328 29396130 30248998 851568 853977 60 37 | ctg10l 50517107 21275071 21525371 - chr1 248387328 30250601 30504483 249743 254087 60 38 | ctg10l 50517107 20117222 21272784 - chr1 248387328 30505648 31665071 1153049 1160575 60 39 | ctg10l 50517107 15661204 20116852 - chr1 248387328 31665375 36130575 4449380 4468755 60 40 | ctg10l 50517107 10376698 15661101 - chr1 248387328 36130907 41414985 5273607 5290685 60 41 | ctg10l 50517107 9534818 10376214 - chr1 248387328 41415163 42256171 839469 842122 60 42 | ctg10l 50517107 8326853 9534759 - chr1 248387328 42256248 43463857 1206492 1208327 60 43 | ctg10l 50517107 7124982 8326165 - chr1 248387328 43464677 44665982 1199402 1202075 60 44 | ctg10l 50517107 1528619 7124022 - chr1 248387328 44666893 50261372 5586617 5599166 60 45 | ctg10l 50517107 2385 1528274 - chr1 248387328 50261502 51787770 1525010 1526721 60 46 | ctg03l 85579487 2433 3759307 + chr1 248387328 51788020 55545054 3751065 3759853 60 47 | ctg03l 85579487 3763408 11496493 + chr1 248387328 55549268 63275880 7713939 7739767 60 48 | ctg03l 85579487 11496575 12470196 + chr1 248387328 63276019 64249437 972265 973993 60 49 | ctg03l 85579487 12470431 14756415 + chr1 248387328 64249671 66537663 2280623 2290627 60 50 | ctg03l 85579487 14756506 20023753 + chr1 248387328 66537869 71806279 5259587 5271693 60 51 | ctg03l 85579487 20023930 35023002 + chr1 248387328 71807010 86825966 14977467 15028035 60 52 | ctg03l 85579487 35023157 37837911 + chr1 248387328 86826152 89640998 2810368 2816416 60 53 | ctg03l 85579487 37838052 38419112 + chr1 248387328 89641288 90222273 580355 581271 60 54 | ctg03l 85579487 38419265 39137224 + chr1 248387328 90222842 90940138 716599 718210 60 55 | ctg03l 85579487 39137328 46552999 + chr1 248387328 90941327 98351375 7400065 7420012 60 56 | ctg03l 85579487 46553281 49607007 + chr1 248387328 98351579 101402331 3045097 3056504 60 57 | ctg03l 85579487 49607788 51249724 + chr1 248387328 101403303 103044959 1638936 1642888 60 58 | ctg03l 85579487 51249830 54109279 + chr1 248387328 103045040 105997624 2854017 2955739 60 59 | ctg03l 85579487 54109328 56460313 + chr1 248387328 105997624 108343966 2343513 2351755 60 60 | ctg03l 85579487 56633521 56921470 + chr1 248387328 108516786 108804693 287363 288182 60 61 | ctg03l 85579487 56921755 58250062 + chr1 248387328 108805088 110130639 1322022 1330803 60 62 | ctg03l 85579487 58251317 61547355 + chr1 248387328 110133501 113427605 3288900 3298216 60 63 | ctg03l 85579487 61547214 68459742 + chr1 248387328 113427564 120336348 6899489 6916499 60 64 | ctg03l 85579487 68705741 69754851 + chr1 248387328 120588838 121633696 1040313 1052079 60 65 | ctg03l 85579487 74481940 75054776 + chr1 248387328 126300406 126634702 329667 573539 60 66 | ctg03l 85579487 75135255 75339521 + chr1 248387328 126647861 126847480 197237 205752 60 67 | ctg11l 120605123 6860416 7219966 + chr1 248387328 128741350 129042480 300306 360033 60 68 | ctg11l 120605123 13050207 13317074 + chr1 248387328 136621294 136937231 244372 337516 60 69 | ctg11l 120605123 13452264 13610193 + chr1 248387328 138467084 138622789 139261 173917 60 70 | ctg11l 120605123 13770002 14025620 + chr1 248387328 141601076 141854031 203422 304408 60 71 | ctg11l 120605123 14029567 14143427 + chr1 248387328 141863426 141982835 106420 126381 60 72 | ctg11l 120605123 14318473 15295191 + chr1 248387328 142172839 143148444 963972 987638 60 73 | ctg11l 120605123 15343500 15636548 + chr1 248387328 143200850 143493975 292621 293301 60 74 | ctg11l 120605123 15810694 17793048 + chr1 248387328 143647790 145602144 1922960 2011869 60 75 | ctg11l 120605123 18052860 23539066 + chr1 248387328 145852545 151336840 5474752 5490481 60 76 | ctg11l 120605123 23539199 29246766 + chr1 248387328 151338383 157054826 5698246 5721462 60 77 | ctg11l 120605123 29246802 32312585 + chr1 248387328 157054862 160122109 3061862 3068578 60 78 | ctg11l 120605123 32383515 39159114 + chr1 248387328 160193433 166964928 6758958 6780345 60 79 | ctg11l 120605123 39159344 40022085 + chr1 248387328 166965186 167825161 859054 863128 60 80 | ctg11l 120605123 40024321 40832959 + chr1 248387328 167826995 168635990 806925 809525 60 81 | ctg11l 120605123 40907512 41561187 + chr1 248387328 168710594 169363966 652542 653884 60 82 | ctg11l 120605123 41561656 44248123 + chr1 248387328 169364434 172051277 2682795 2688139 60 83 | ctg11l 120605123 44248459 46614993 + chr1 248387328 172052065 174413441 2358889 2367613 60 84 | ctg11l 120605123 46615092 46786806 + chr1 248387328 174413528 174585370 171390 171903 60 85 | ctg11l 120605123 46787362 47536801 + chr1 248387328 174585764 175335541 748507 750122 60 86 | ctg11l 120605123 47536860 48955179 + chr1 248387328 175335615 176753824 1416475 1418842 60 87 | ctg11l 120605123 48955515 50252004 + chr1 248387328 176753980 178050257 1294642 1297085 60 88 | ctg11l 120605123 50253001 52637166 + chr1 248387328 178051101 180429442 2374700 2385607 60 89 | ctg11l 120605123 52637886 57889870 + chr1 248387328 180429686 185681748 5236865 5263492 60 90 | ctg11l 120605123 57890030 64724523 + chr1 248387328 185681871 192508839 6818849 6837834 60 91 | ctg11l 120605123 64724644 65126683 + chr1 248387328 192508980 192912813 401389 404144 60 92 | ctg11l 120605123 65126853 65661802 + chr1 248387328 192912920 193447689 533983 535153 60 93 | ctg11l 120605123 65662206 69349374 + chr1 248387328 193448171 197047049 3592207 3690125 60 94 | ctg11l 120605123 69350569 71049462 + chr1 248387328 197048245 198735704 1685368 1699641 60 95 | ctg11l 120605123 71049628 73743965 + chr1 248387328 198735857 201430066 2690470 2695801 60 96 | ctg11l 120605123 73744308 74247140 + chr1 248387328 201430275 201934539 501842 504763 60 97 | ctg11l 120605123 74247222 76785615 + chr1 248387328 201934534 204473862 2534034 2540991 60 98 | ctg11l 120605123 76785776 78693406 + chr1 248387328 204473943 206384250 1904805 1911885 60 99 | ctg11l 120605123 78693519 86385912 + chr1 248387328 206385101 214073246 7674778 7699925 60 100 | ctg11l 120605123 86387289 87297089 + chr1 248387328 214074005 214983765 909278 909985 60 101 | ctg11l 120605123 87297185 89078705 + chr1 248387328 214983835 216765934 1778896 1783040 60 102 | ctg11l 120605123 89079179 90222707 + chr1 248387328 216766257 217909818 1142332 1143947 60 103 | ctg11l 120605123 90222698 104328921 + chr1 248387328 217909811 232111201 14081529 14213604 60 104 | ctg11l 120605123 104328976 104943677 + chr1 248387328 232111248 232725635 613630 614940 60 105 | ctg11l 120605123 104943614 105711530 + chr1 248387328 232725611 233494699 765975 769893 60 106 | ctg11l 120605123 105711687 110251176 + chr1 248387328 233494783 238038960 4524015 4554748 60 107 | ctg11l 120605123 110251363 112689070 + chr1 248387328 238039098 240472272 2428283 2440638 60 108 | ctg11l 120605123 112689125 115154185 + chr1 248387328 240472327 242937839 2461186 2467115 60 109 | ctg11l 120605123 115154352 117888657 + chr1 248387328 242937930 245669551 2724000 2738843 60 110 | ctg11l 120605123 117888720 118335819 + chr1 248387328 245669606 246115586 443203 449189 60 111 | ctg11l 120605123 118340530 118466029 + chr1 248387328 246119120 246245676 125294 126603 60 112 | ctg11l 120605123 118470405 118746984 + chr1 248387328 246247583 246523030 274380 277402 60 113 | ctg11l 120605123 118747143 120594994 + chr1 248387328 246523109 248383457 1833692 1872422 60 114 | -------------------------------------------------------------------------------- /example/test1.paf.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moold/paf2dotplot/43b39f0d2c01bad5b272854e73e35792667a21e9/example/test1.paf.png -------------------------------------------------------------------------------- /example/test2.paf.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moold/paf2dotplot/43b39f0d2c01bad5b272854e73e35792667a21e9/example/test2.paf.png -------------------------------------------------------------------------------- /paf2dotplot.r: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env Rscript 2 | 3 | suppressPackageStartupMessages(library(optparse)) 4 | suppressPackageStartupMessages(library(ggplot2)) 5 | 6 | option_list <- list( 7 | make_option(c("-o","--output"), type="character", 8 | help="output filename prefix [input.paf]", 9 | dest="output_filename"), 10 | make_option(c("-p","--plot-size"), type="numeric", default=15, 11 | help="plot size X inches [%default]", 12 | dest="plot_size"), 13 | make_option(c("-f","--flip"), action="store_true", default=FALSE, 14 | help="flip query if most alignments are in reverse complement [%default]", 15 | dest="flip"), 16 | make_option(c("-b","--break-point"), action="store_true", default=FALSE, 17 | help="show break points [%default]", 18 | dest="break_point"), 19 | make_option(c("-c","--identity-lower-color"), type="numeric", default=0, 20 | help="percent identity that lower than this value will be assigned the same color [%default]", 21 | dest="identity_lower"), 22 | make_option(c("-s", "--sort-by-refid"), action="store_true", default=FALSE, 23 | help="sort reference IDs in alphabetical order, default by length [%default]", 24 | dest="sortbyID"), 25 | make_option(c("-q", "--min-query-length"), type="numeric", default=400000, 26 | help="filter queries with total alignments less than cutoff X bp [%default]", 27 | dest="min_query_aln"), 28 | make_option(c("-m", "--min-alignment-length"), type="numeric", default=10000, 29 | help="filter alignments less than cutoff X bp [%default]", 30 | dest="min_align"), 31 | make_option(c("-r", "--min-ref-len"), type="numeric", default=1000000, 32 | help="filter references with length less than cutoff X bp [%default]", 33 | dest="min_ref_len"), 34 | make_option(c("-i", "--reference-ids"), type="character", default=NULL, 35 | help="comma-separated list of reference IDs to keep and order [%default]", 36 | dest="refIDs") 37 | ) 38 | 39 | options(error=traceback) 40 | parser <- OptionParser(usage = "%prog [options] input.paf\n\nFor more information, see https://github.com/moold/paf2dotplot", option_list = option_list) 41 | opts = parse_args(parser, positional_arguments = c(0, 1)) 42 | opt = opts$options 43 | input_file = opts$args 44 | if(length(input_file) <= 0){ 45 | cat(sprintf("Error: missing input file: input.paf!\n\n")) 46 | print_help(parser) 47 | quit() 48 | }else if (file.access(input_file, mode=4) == -1){ 49 | cat(sprintf("Error: input file: %s does not exist or cannot be read!\n\n", input_file)) 50 | print_help(parser) 51 | quit() 52 | } 53 | if(is.null(opt$output_filename)){ 54 | opt$output_filename = input_file 55 | } 56 | 57 | # read in alignments 58 | alignments = read.table(input_file, stringsAsFactors = F, row.names=NULL, fill = T, header = F)[, c(1:12)] 59 | # avoid inter overflow 60 | alignments[, c(2:4, 7:12)] = apply(alignments[, c(2:4, 7:12)], 2, as.double) 61 | 62 | # set column names 63 | # PAF IS ZERO-BASED - CHECK HOW CODE WORKS 64 | colnames(alignments)[1:12] = c("queryID","queryLen","queryStart","queryEnd","strand","refID","refLen","refStart","refEnd","numResidueMatches","lenAln","mapQ") 65 | 66 | # caculate similarity 67 | alignments$percentID = alignments$numResidueMatches / alignments$lenAln 68 | if (opt$identity_lower) { 69 | alignments$percentID[which(alignments$percentID < opt$identity_lower)] <- opt$identity_lower 70 | } 71 | 72 | queryStartTemp = alignments$queryStart 73 | # Flip starts, ends for negative strand alignments 74 | alignments$queryStart[which(alignments$strand == "-")] = alignments$queryEnd[which(alignments$strand == "-")] 75 | alignments$queryEnd[which(alignments$strand == "-")] = queryStartTemp[which(alignments$strand == "-")] 76 | rm(queryStartTemp) 77 | 78 | cat(paste0("\nNumber of alignments: ", nrow(alignments), "\n")) 79 | cat(paste0("Number of query sequences: ", length(unique(alignments$queryID)), "\n")) 80 | 81 | # sort by ref chromosome sizes, keep top X chromosomes OR keep specified IDs 82 | if(is.null(opt$refIDs)){ 83 | if (opt$sortbyID){ 84 | refIDsToKeepOrdered = unique(sort(alignments$refID)) 85 | }else{ 86 | chromMax = tapply(alignments$refLen, alignments$refID, max) 87 | refIDsToKeepOrdered = names(sort(chromMax, decreasing = T)) 88 | } 89 | }else{ 90 | refIDsToKeepOrdered = unlist(strsplit(opt$refIDs, ",")) 91 | alignments = alignments[which(alignments$refID %in% refIDsToKeepOrdered),] 92 | } 93 | 94 | # filter queries by alignment length, for now include overlapping intervals 95 | queryLenAgg = tapply(alignments$lenAln, alignments$queryID, sum) 96 | alignments = alignments[which(alignments$queryID %in% names(queryLenAgg)[which(queryLenAgg > opt$min_query_aln)]),] 97 | # filter alignment by length 98 | alignments = alignments[which(alignments$lenAln > opt$min_align),] 99 | # filter alignment by ref length 100 | alignments = alignments[which(alignments$refLen > opt$min_ref_len),] 101 | # re-filter queries by alignment length, for now include overlapping intervals 102 | queryLenAgg = tapply(alignments$lenAln, alignments$queryID, sum) 103 | alignments = alignments[which(alignments$queryID %in% names(queryLenAgg)[which(queryLenAgg > opt$min_query_aln)]),] 104 | 105 | cat(paste0("\nAfter filtering... Number of alignments: ", nrow(alignments),"\n")) 106 | cat(paste0("After filtering... Number of query sequences: ", length(unique(alignments$queryID)),"\n\n")) 107 | 108 | if (nrow(alignments) == 0) { 109 | cat("Error: All alignments were discarded after filtering, no valid alignments remain.\n\n.") 110 | quit() 111 | } 112 | 113 | # filter refIDsToKeepOrdered if some refID are filtered 114 | refIDsToKeepOrdered = refIDsToKeepOrdered[which(refIDsToKeepOrdered %in% alignments$refID)] 115 | 116 | # sort df on ref 117 | alignments$refID = factor(alignments$refID, levels = refIDsToKeepOrdered) # set order of refID 118 | alignments = alignments[with(alignments,order(refID,refStart)),] 119 | chromMax = tapply(alignments$refLen, alignments$refID, max) 120 | # make new ref alignments for dot plot 121 | 122 | alignments$refStart2 = alignments$refStart + sapply(as.character(alignments$refID), function(x) ifelse(x == names(chromMax)[1], 0, cumsum(as.numeric(chromMax))[match(x, names(chromMax)) - 1]) ) 123 | alignments$refEnd2 = alignments$refEnd + sapply(as.character(alignments$refID), function(x) ifelse(x == names(chromMax)[1], 0, cumsum(as.numeric(chromMax))[match(x, names(chromMax)) - 1]) ) 124 | 125 | ## queryID sorting step 1/2 126 | # sort levels of factor 'queryID' based on longest alignment 127 | alignments$queryID = factor(alignments$queryID, levels=unique(as.character(alignments$queryID))) 128 | queryMaxAlnIndex = tapply(alignments$lenAln, alignments$queryID, which.max, simplify = F) 129 | alignments$queryID = factor(alignments$queryID, levels = unique(as.character(alignments$queryID))[order(mapply( 130 | function(x, i) 131 | alignments$refStart2[which(i == alignments$queryID)][x], 132 | queryMaxAlnIndex, 133 | names(queryMaxAlnIndex) 134 | ))]) 135 | 136 | ## queryID sorting step 2/2 137 | ## sort levels of factor 'queryID' based on longest aggregrate alignmentst to refID's 138 | # per query ID, get aggregrate alignment length to each refID 139 | queryLenAggPerRef = sapply((levels(alignments$queryID)), function(x) tapply(alignments$lenAln[which(alignments$queryID == x)], alignments$refID[which(alignments$queryID == x)], sum) ) 140 | if(length(levels(alignments$refID)) > 1){ 141 | queryID_Ref = apply(queryLenAggPerRef, 2, function(x) rownames(queryLenAggPerRef)[which.max(x)]) 142 | } else { 143 | queryID_Ref = sapply(queryLenAggPerRef, function(x) names(queryLenAggPerRef)[which.max(x)]) 144 | } 145 | # set order for queryID 146 | alignments$queryID = factor(alignments$queryID, levels = (levels(alignments$queryID))[order(match(queryID_Ref, levels(alignments$refID)))]) 147 | queryMax = tapply(alignments$queryLen, alignments$queryID, max) 148 | 149 | if(opt$flip){ 150 | # flip query starts stops to forward if most align are in reverse complement 151 | queryRevComp = tapply(alignments$queryEnd - alignments$queryStart, alignments$queryID, function(x) sum(x)) < 0 152 | queryRevComp = names(queryRevComp)[which(queryRevComp)] 153 | alignments$queryStart[which(alignments$queryID %in% queryRevComp)] = queryMax[match(as.character(alignments$queryID[which(alignments$queryID %in% queryRevComp)]), names(queryMax))] - alignments$queryStart[which(alignments$queryID %in% queryRevComp)] + 1 154 | alignments$queryEnd[which(alignments$queryID %in% queryRevComp)] = queryMax[match(as.character(alignments$queryID[which(alignments$queryID %in% queryRevComp)]), names(queryMax))] - alignments$queryEnd[which(alignments$queryID %in% queryRevComp)] + 1 155 | } 156 | ## make new query alignments for dot plot 157 | alignments$queryStart2 = alignments$queryStart + sapply(as.character(alignments$queryID), function(x) ifelse(x == names(queryMax)[1], 0, cumsum(queryMax)[match(x, names(queryMax)) - 1]) ) 158 | alignments$queryEnd2 = alignments$queryEnd + sapply(as.character(alignments$queryID), function(x) ifelse(x == names(queryMax)[1], 0, cumsum(queryMax)[match(x, names(queryMax)) - 1]) ) 159 | 160 | # plot break points 161 | if (opt$break_point) { 162 | alignments$break_col = rep(0, length(alignments$percentID)); 163 | } 164 | 165 | options(warn = -1) # turn off warnings 166 | gp = ggplot(alignments) + 167 | theme_bw() + 168 | theme( 169 | text = element_text(size = 12), 170 | panel.grid.minor.y = element_blank(), 171 | panel.grid.minor.x = element_blank(), 172 | axis.text.y = element_text(angle = 15), 173 | axis.text.x = element_text(hjust = 1, angle = 45) 174 | ) + 175 | scale_color_distiller(palette = "Spectral") + 176 | labs(color = "Identity", 177 | title = paste0(paste0("Post-filtering number of alignments: ", nrow(alignments),"\t\t\t\t"), 178 | paste0("minimum alignment length (-m): ", opt$min_align,"\n"), 179 | paste0("Post-filtering number of queries: ", length(unique(alignments$queryID)),"\t\t\t\t\t\t\t\t"), 180 | paste0("minimum query aggregate alignment length (-q): ", opt$min_query_aln) 181 | ) 182 | ) 183 | 184 | # x 185 | if (length(unique(alignments$refID)) == 1){ 186 | reflen = unique(alignments$refLen) 187 | xbreaks = seq(0, reflen, reflen/10) 188 | if (reflen/10 > 1e9){ 189 | xlables = paste(round(xbreaks/1e9), "GB") 190 | }else if (reflen/10 > 1e6) { 191 | xlables = paste(round(xbreaks/1e6), "MB") 192 | }else if(reflen/10 > 1e3){ 193 | xlables = paste(round(xbreaks/1e3), "KB") 194 | }else{ 195 | xlables = paste(round(xbreaks), "bp") 196 | } 197 | 198 | gp = gp + scale_x_continuous(expand = c(0, 0), limits = c(0, reflen + 0.1), breaks = xbreaks, labels = xlables) + 199 | xlab(unique(alignments$refID)) 200 | }else{ 201 | gp = gp + 202 | theme(panel.grid.major.x=element_blank()) + 203 | geom_vline(xintercept = cumsum(as.numeric(chromMax)), col="#ebebeb") + 204 | scale_x_continuous(expand = c(0, 0), limits = c(0, sum(as.numeric(chromMax)) + 0.1), 205 | breaks = cumsum(as.numeric(chromMax)) - chromMax/2, labels = substr(levels(alignments$refID), start = 1, stop = 20)) + 206 | xlab("Reference") 207 | } 208 | 209 | # y 210 | if (length(unique(alignments$queryID)) == 1){ 211 | queryLen = unique(alignments$queryLen) 212 | ybreaks = seq(0, queryLen, queryLen/10) 213 | if (queryLen/10 > 1e9){ 214 | ylables = paste(round(ybreaks/1e9), "GB") 215 | }else if (queryLen/10 > 1e6) { 216 | ylables = paste(round(ybreaks/1e6), "MB") 217 | }else if(queryLen/10 > 1e3){ 218 | ylables = paste(round(ybreaks/1e3), "KB") 219 | }else{ 220 | ylables = paste(round(ybreaks), "bp") 221 | } 222 | 223 | gp = gp + scale_y_continuous(expand = c(0, 0), limits = c(0, queryLen + 0.1), breaks = ybreaks, labels = ylables) + 224 | ylab(unique(alignments$queryID)) 225 | }else{ 226 | gp = gp + 227 | theme(panel.grid.major.y=element_blank()) + 228 | geom_hline(yintercept = cumsum(as.numeric(queryMax)), col="#ebebeb") + 229 | scale_y_continuous(expand = c(0, 0), limits = c(0, sum(as.numeric(queryMax)) + 0.1), 230 | breaks = cumsum(as.numeric(queryMax)) - queryMax/2, labels = substr(levels(alignments$queryID), start = 1, stop = 20)) + 231 | ylab("Query") 232 | } 233 | 234 | # plot co-line 235 | gp = gp + geom_segment(aes(x = refStart2, xend = refEnd2, y = queryStart2, yend = queryEnd2, color = percentID)) 236 | 237 | # plot break points 238 | if (opt$break_point) { 239 | gp = gp + geom_point(mapping = aes(x = refStart2, y = queryStart2, color = break_col), size = opt$plot_size/60, shape = 19) + 240 | geom_point(mapping = aes(x = refEnd2, y = queryEnd2, color = break_col), size = opt$plot_size/60, shape = 19) 241 | } 242 | 243 | # save 244 | ggsave(filename = paste0(opt$output_filename, ".pdf"), width = opt$plot_size, height = opt$plot_size * 0.8, units = "in", dpi = 300, limitsize = F) 245 | options(warn=0) # turn on warnings 246 | --------------------------------------------------------------------------------