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stephenturner / qqman

An R package for creating Q-Q and manhattan plots from GWAS results
http://cran.r-project.org/web/packages/qqman/
GNU General Public License v3.0
154 stars 92 forks source link

Error in plot.window(...) : need finite 'ylim' values #34

Closed Adisha05 closed 8 years ago

Adisha05 commented 8 years ago

Having an issue with qqman when trying to plot manhattan plots A<-read.table("input.txt", header=T) B<-read.table("Highlight.txt", header=T) manhattan(A, chr = "CHR", bp = "BP", p = "P", snp = "SNP",col = c("gray10", "gray60"), chrlabs = NULL,highlight = B, logp = TRUE)

input.txt image

Highlight.txt

image

stephenturner commented 8 years ago

the screenshots aren't helping me. upload your data to https://gist.github.com/ and paste a link here.

Adisha05 commented 8 years ago

Hey stephen, here is the link https://gist.github.com/Adisha05/094561736496076dd2d0

stephenturner commented 8 years ago

Works for me.

library(qqman)

# Load data
d <- read.table("input.txt", header=T)
snps <- readLines("Highlight.txt")

# Try making the plot
manhattan(d,highlight=snps)
# clear what problem is from error message

# restrict snps of interest to those that
# actually exist in the data
snps <- snps[snps %in% d$SNP]

# try again
manhattan(d,highlight=snps)

image

Adisha05 commented 8 years ago

It works fine with this small data. But I can't see any highlighted SNPs with a bigger data file. Does it have something to do with the P-value or do i need to scale the graph? In the attached file "Highlight.txt" I can only see the top 5 SNPs in the manhattan plot and not the bottom 5. https://gist.github.com/4cea1b9ba9bf3081a065.git

stephenturner commented 8 years ago

@Adisha05 please leave a reproducible example here, not on the blog comments. Thanks.

stephenturner commented 8 years ago

Please leave a reproducible example here.

On Fri, Oct 30, 2015 at 4:54 AM, Adisha05 notifications@github.com wrote:

It works fine with this small data. But I can't see any highlighted SNPs with a bigger data file. Does it have something to do with the P-value or do i need to scale the graph? In the attached file "Highlight.txt" I can only see the top 5 SNPs in the manhattan plot and not the bottom 5.

— Reply to this email directly or view it on GitHub https://github.com/stephenturner/qqman/issues/34#issuecomment-152463167.

Adisha05 commented 8 years ago

It works fine with this small data. But I can't see any highlighted SNPs with a bigger data file. Does it have something to do with the P-value or do i need to scale the graph? In the attached file "Highlight.txt" I can only see the top 5 SNPs in the manhattan plot and not the bottom 5.

Highlight.txt SNP A1 A2 A3 A4 A5 A2501 A2502 A2503 A2504 A2505

Input.txt

SNP CHR BP P A1 1 55745487 6.17E-05 A2 1 9098899 8.93E-05 A3 1 51859932 0.000221529 A4 1 151530116 0.000429329 A5 1 64054878 0.000592133 A6 1 68510269 0.00063433 A7 1 29885949 0.000716833 A8 1 104120824 0.00089851 A9 1 63057541 0.001024774 A10 1 143370557 0.001362536 A11 1 135219501 0.001363977 A12 1 63793607 0.001481604 A13 1 71563554 0.001887271 A14 1 93311609 0.002253141 A15 1 73119195 0.002262499 A16 1 150844776 0.00228538 A17 1 63528234 0.002594162 A18 1 104238168 0.002626313 A19 1 50531107 0.002916178 A20 1 65366739 0.002983276 A21 1 109087579 0.003026952 A22 1 127157375 0.003028225 A23 1 92568843 0.003105712 A24 1 51737682 0.003276138 A25 1 29219133 0.00394106 A26 1 114010038 0.003943638 A27 1 17145973 0.004209814 A28 1 21837257 0.004374444 A29 1 157372290 0.004389251 A30 1 47016798 0.004451327 A31 1 115795297 0.004763636 A32 1 16068791 0.004940353 A33 1 101604609 0.005178532 A34 1 123818604 0.005408429 A35 1 72472612 0.005456555 A36 1 33799177 0.005475667 A37 1 110016500 0.005477567 A38 1 26518094 0.005546007 A39 1 34347534 0.005621287 A40 1 29830062 0.005979968 A41 1 26876167 0.006112039 A42 1 135771216 0.006251334 A43 1 70234224 0.006295581 A44 1 7106052 0.006552946 A45 1 137595625 0.006961712 A46 1 10387987 0.007117944 A47 1 123704791 0.007133577 A48 1 111745802 0.007229572 A49 1 137980068 0.007369506 A50 1 64173387 0.007391014 A51 1 121969702 0.007651796 A52 1 44640564 0.007671467 A53 1 33711421 0.007702702 A54 1 71660196 0.007766927 A55 1 137680051 0.007978492 A56 1 123776732 0.008054264 A57 1 130593853 0.00819702 A58 1 123753533 0.008270054 A59 1 5417032 0.008286568 A60 1 20399664 0.008503231 A61 1 26710108 0.008536869 A62 1 34407163 0.008574748 A63 1 126562286 0.008722473 A64 1 37667471 0.008773341 A65 1 51389104 0.008793626 A66 1 13606082 0.008840847 A67 1 84722207 0.009005277 A68 1 88181050 0.009092748 A69 1 124105379 0.009299499 A70 1 78205574 0.009318969 A71 1 72565211 0.00942996 A72 1 148211653 0.009571703 A73 1 132160170 0.009585145 A74 1 112691945 0.009750937 A75 1 122157745 0.009904529 A76 1 139935237 0.010159747 A77 1 73154504 0.01033371 A78 1 108250420 0.010337452 A79 1 9056807 0.010519629 A80 1 90611547 0.010560994 A81 1 52795445 0.010564583 A82 1 109836861 0.010595704 A83 1 62159476 0.010799235 A84 1 118986154 0.010814543 A85 1 94052770 0.011033777 A86 1 143026659 0.011039858 A87 1 73357204 0.011127726 A88 1 139394134 0.011161073 A89 1 55513137 0.011424862 A90 1 13519841 0.011458398 A91 1 133558742 0.011598178 A92 1 104337951 0.011676353 A93 1 110036619 0.011685014 A94 1 158796317 0.011728546 A95 1 149983558 0.011761488 A96 1 101468706 0.011856997 A97 1 34458788 0.012378599 A98 1 91406644 0.012488073 A99 1 53366756 0.012709535 A100 1 118767792 0.012788281 A101 1 141618695 0.013259823 A102 1 29975904 0.013271578 A103 1 65712986 0.013584682 A104 1 48503468 0.013774854 A105 1 33047885 0.01385202 A106 1 153540793 0.013941245 A107 1 103737794 0.013963234 A108 1 66098174 0.014033053 A109 1 38277857 0.014098661 A110 1 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0.990768392 A2253 1 134111439 0.991200146 A2254 1 100309214 0.991730192 A2255 1 29712572 0.993318546 A2256 1 41168632 0.994042142 A2257 1 61377409 1.00489649 A2258 1 140685650 1.006949358 A2259 1 43082466 1.01219912 A2260 1 74435893 1.012915602 A2261 1 125056616 1.013103896 A2262 1 125218596 1.013383411 A2263 1 152817114 1.01616687 A2264 1 42714935 1.020053714 A2265 1 3176764 1.020913012 A2266 1 103275173 1.026426646 A2267 1 59323900 1.027327025 A2268 1 154551517 1.029850568 A2269 1 142695857 1.032003191 A2270 1 100287967 1.037678616 A2271 1 105572914 1.037936668 A2272 1 138480229 1.045373986 A2273 1 80419711 1.046711852 A2274 1 94216215 1.04679001 A2275 1 38952266 1.046972616 A2276 1 97034901 1.046987235 A2277 1 16887708 1.049171386 A2278 1 23503624 1.052075377 A2279 1 20870762 1.052441338 A2280 1 67755812 1.054141612 A2281 1 86222950 1.054823591 A2282 1 130097031 1.057137042 A2283 1 69643960 1.060110054 A2284 1 67210807 1.063698156 A2285 1 22292405 1.063840946 A2286 1 100026598 1.067900613 A2287 1 127624399 1.069271223 A2288 1 123089929 1.0697566 A2289 1 144378177 1.072794163 A2290 1 71127523 1.075709369 A2291 1 16828640 1.077967482 A2292 1 20933177 1.079637134 A2293 1 35610743 1.080366914 A2294 1 129147032 1.080452123 A2295 1 84438164 1.082359946 A2296 1 68220456 1.082999232 A2297 1 22184888 1.088036231 A2298 1 96744251 1.092889283 A2299 1 107238266 1.092950804 A2300 1 21224195 1.094270924 A2301 1 6590362 1.094548265 A2302 1 32308255 1.094784915 A2303 1 36404483 1.094975776 A2304 1 83575091 1.097492562 A2305 1 19179351 1.098458483 A2306 1 83793211 1.101062703 A2307 1 114544238 1.102367997 A2308 1 149211910 1.103741619 A2309 1 125168157 1.106487462 A2310 1 75042635 1.11138624 A2311 1 103536856 1.112350038 A2312 1 147524968 1.115178925 A2313 1 74540503 1.1202392 A2314 1 81856896 1.121590895 A2315 1 100368341 1.125257158 A2316 1 105550683 1.13108907 A2317 1 60394452 1.131518046 A2318 1 148770165 1.137901474 A2319 1 85746256 1.138422577 A2320 1 21892255 1.138607262 A2321 1 116445187 1.140862301 A2322 1 41020597 1.140967508 A2323 1 118422823 1.145813503 A2324 1 42106878 1.145856512 A2325 1 75135241 1.145864296 A2326 1 19802295 1.147030548 A2327 1 23551249 1.151726581 A2328 1 32334089 1.156976834 A2329 1 32364122 1.156976834 A2330 1 84365429 1.16208568 A2331 1 100339279 1.169091082 A2332 1 74208849 1.172438618 A2333 1 128294157 1.174761505 A2334 1 73730134 1.177809686 A2335 1 11939028 1.180628311 A2336 1 128315628 1.183006601 A2337 1 100510062 1.183701757 A2338 1 149116418 1.189618097 A2339 1 67726747 1.193957586 A2340 1 97068957 1.195617209 A2341 1 112143240 1.195641566 A2342 1 17106220 1.196888708 A2343 1 67147487 1.201154162 A2344 1 103377349 1.20210349 A2345 1 30729602 1.204405531 A2346 1 158029768 1.206495641 A2347 1 3434513 1.212143437 A2348 1 83751110 1.219928249 A2349 1 88336773 1.222213936 A2350 1 43173390 1.22333896 A2351 1 43137144 1.233441095 A2352 1 138526829 1.238992733 A2353 1 76602613 1.239956996 A2354 1 138561548 1.246706095 A2355 1 54801753 1.248336271 A2356 1 85244393 1.24852431 A2357 1 22253338 1.254455995 A2358 1 140876203 1.268914608 A2359 1 103095846 1.270880088 A2360 1 129075420 1.279040452 A2361 1 81789611 1.281583212 A2362 1 21300410 1.290969657 A2363 1 138702883 1.291967765 A2364 1 99940814 1.294872422 A2365 1 23317322 1.300926822 A2366 1 155991206 1.304688214 A2367 1 1324141 1.305328356 A2368 1 100223105 1.311975034 A2369 1 134025807 1.323583468 A2370 1 2809422 1.323822148 A2371 1 80314814 1.328567281 A2372 1 83718411 1.336029807 A2373 1 144271780 1.341207796 A2374 1 140847628 1.341460071 A2375 1 96772614 1.347907385 A2376 1 85439533 1.347936144 A2377 1 110940741 1.352005436 A2378 1 44861514 1.358775732 A2379 1 123888829 1.359360895 A2380 1 1897417 1.361515626 A2381 1 125264326 1.361579176 A2382 1 48097918 1.370035307 A2383 1 140706548 1.375843567 A2384 1 67173004 1.381179911 A2385 1 48327004 1.385787028 A2386 1 44840250 1.389620217 A2387 1 41042734 1.395789042 A2388 1 10143920 1.400002339 A2389 1 39692199 1.408155718 A2390 1 54738191 1.411093507 A2391 1 148911817 1.41138875 A2392 1 107291207 1.413035305 A2393 1 3211001 1.423562082 A2394 1 85694936 1.424681423 A2395 1 74957977 1.425833439 A2396 1 67627871 1.436461375 A2397 1 59607413 1.442555343 A2398 1 149189841 1.444254239 A2399 1 10122355 1.44921872 A2400 1 17012359 1.454935026 A2401 1 29700548 1.461198014 A2402 1 74016191 1.461897325 A2403 1 1393698 1.472364529 A2404 1 21044560 1.476218021 A2405 1 116476338 1.477556987 A2406 1 96957948 1.490047081 A2407 1 23195769 1.509479939 A2408 1 149000570 1.509570028 A2409 1 116539265 1.509876926 A2410 1 144161247 1.517087911 A2411 1 42906016 1.523040626 A2412 1 21093246 1.531778916 A2413 1 103167665 1.532482745 A2414 1 23052105 1.537467302 A2415 1 114569287 1.554600854 A2416 1 74255433 1.569825462 A2417 1 9825544 1.574094815 A2418 1 103459113 1.57465634 A2419 1 103577744 1.577741859 A2420 1 152153087 1.584621475 A2421 1 125015815 1.588610833 A2422 1 60513894 1.593006003 A2423 1 1416454 1.598269342 A2424 1 87845374 1.599576669 A2425 1 99686393 1.603535199 A2426 1 1857163 1.60392586 A2427 1 8015127 1.60762241 A2428 1 60548241 1.623161149 A2429 1 69576518 1.631310963 A2430 1 130073476 1.638832717 A2431 1 74923746 1.647699673 A2432 1 68762710 1.648592423 A2433 1 54717465 1.649410203 A2434 1 1354280 1.669011784 A2435 1 64825089 1.67101862 A2436 1 73786757 1.67418835 A2437 1 3268723 1.681549011 A2438 1 21919792 1.684878023 A2439 1 107572909 1.694431975 A2440 1 34054462 1.697767835 A2441 1 131867215 1.721287844 A2442 1 138661649 1.732723515 A2443 1 68709076 1.752506968 A2444 1 16801749 1.761807185 A2445 1 80362915 1.772790351 A2446 1 138457513 1.772959059 A2447 1 3239884 1.786101124 A2448 1 100434165 1.790236012 A2449 1 9894290 1.793662178 A2450 1 128561273 1.814824497 A2451 1 128564262 1.845258737 A2452 1 35197090 1.850212126 A2453 1 103004837 1.853674948 A2454 1 103059783 1.853873399 A2455 1 1570768 1.860886449 A2456 1 85642599 1.87764772 A2457 1 111058352 1.908813535 A2458 1 2688379 1.936879974 A2459 1 10075525 1.944052208 A2460 1 100261283 1.951503949 A2461 1 144230610 1.964153345 A2462 1 138602575 2.009079292 A2463 1 23220897 2.024224678 A2464 1 103356065 2.038683786 A2465 1 149080930 2.06317852 A2466 1 148976411 2.08049659 A2467 1 74129177 2.093446118 A2468 1 148951349 2.142965017 A2469 1 138635745 2.153531728 A2470 1 85988054 2.15427937 A2471 1 2710093 2.209881812 A2472 1 10098307 2.220275826 A2473 1 8044611 2.221484599 A2474 1 149153073 2.232816858 A2475 1 68666222 2.266511205 A2476 1 128975080 2.26921283 A2477 1 66936404 2.276397317 A2478 1 103229117 2.333672516 A2479 1 128882229 2.358770478 A2480 1 1791640 2.376866052 A2481 1 66971784 2.405144018 A2482 1 67055260 2.416422904 A2483 1 84394163 2.455204916 A2484 1 67680630 2.488582071 A2485 1 16985644 2.553404692 A2486 1 128749076 2.60254751 A2487 1 128817537 2.638001157 A2488 1 128725281 2.664546253 A2489 1 128653029 2.684909137 A2490 1 128680930 2.684909137 A2491 1 2741612 2.720218115 A2492 1 103025507 2.906519947 A2493 1 2775726 2.918410998 A2494 1 152125152 3.010382283 A2495 1 67119588 3.079031845 A2496 1 69472455 3.270261858 A2497 1 85888745 3.273383116 A2498 1 128593623 3.281754946 A2499 1 66851552 3.389780691 A2500 1 69528623 3.390342188 A2501 1 85954529 3.399578801 A2502 1 85819755 3.431910518 A2503 1 128625912 3.494069926 A2504 1 67081774 3.59780052 A2505 1 66903182 3.72243979 A2506 1 69443400 3.768098493 A2507 1 9955275 3.820994525 A2508 1 128703087 3.870359939 A2509 1 85798174 3.959785493 A2510 1 1761203 4.161641846 A2511 1 1705124 4.215978276 A2512 1 1662071 4.268319255 A2513 1 1593414 4.386872399 A2514 1 69503257 4.608347382 A2515 1 69551739 4.613490867 A2516 1 1616278 4.729077308 A2517 1 1639320 5.150253119 A2518 1 1729494 5.366972017

Adisha05 commented 8 years ago

Hi Stephen! Is there something that i'm doing wrong here?This is the plot I made using above data. A total of 10 SNPs are there in the text file named Highlight.txt but in the plot i can only see top 5 in green mhplot

stephenturner commented 8 years ago

What seems wrong here?

On Wed, Nov 4, 2015 at 3:48 AM, Adisha05 notifications@github.com wrote:

Hi Stephen! Is there something that i'm doing wrong here?This is the plot I made using above data [image: mhplot] https://cloud.githubusercontent.com/assets/15339350/10933503/3eaa3d26-831c-11e5-9b20-f6afa6183719.png

— Reply to this email directly or view it on GitHub https://github.com/stephenturner/qqman/issues/34#issuecomment-153640928.

Adisha05 commented 8 years ago

I have 10 SNPs to be highlighted (Highlight.txt) but only 5 of them show up in green in the plot. I don't understand why. Ill appreciate any further help.

stephenturner commented 8 years ago

Because the p-values for those SNPs are not between 0 and 1.

     SNP CHR        BP           P
1     A1   1  55745487 0.000061700
2     A2   1   9098899 0.000089300
3     A3   1  51859932 0.000221529
4     A4   1 151530116 0.000429329
5     A5   1  64054878 0.000592133
6  A2501   1  85954529 3.399578801
7  A2502   1  85819755 3.431910518
8  A2503   1 128625912 3.494069926
9  A2504   1  67081774 3.597800520
10 A2505   1  66903182 3.722439790