I'm trying to plot a GWAS (in you will) with lined segments representing an overall p-value for each gene. Here is my code:
skatg <- ggplot(comm, aes(x = position,y = p, colour = grey)) + geom_point(size = 0.75) + geom_segment(data=rare, aes(x = txStart, y = -log10(p), xend=txEnd, yend = -log10(p), colour = darkgreen)) + labs(x = "Position",y = "-log10 P value") + facet_wrap(~ Chrom, scales = "free", ncol = 4) Where comm is a file with 250k+ variants and genes.in.locus is a file with about 18k genes. When running this script, I get the error Don't know how to automatically pick scale for object of type function. Defaulting to continuous Error in data.frame(x = c(40840353L, 31902418L, 19468080L, 236748505L, : arguments imply differing number of rows: 79746, 0 Is this because there are different number of rows in each data frame I'm trying to plot? If so, what is a best way to overcome this error? Example of my data is as follows: comm: Name gene Chrom position p 1 rs10000037 FAM114A1 4 38924330 0.7513597 2 rs10000250 CC2D2A 4 15482477 0.9202882 4 rs10000911 USP38 4 144136193 0.8335902 5 rs10001 STXBP2 19 7711221 0.4709547 7 rs10001370 USP46 4 53463730 0.8759828 8 rs1000152 ZNF462 9 109687288 0.3451001 10 rs10002583 POLN 4 2194953 0.7878575 12 rs10002971 EGF 4 110896050 0.5082255 15 rs10003873 SORBS2 4 186605868 0.2309855 16 rs10003909 ARHGAP24 4 86915848 0.8714853 17 rs10003947 ANXA3 4 79512800 0.5141532 18 rs10004 SSR1 6 7310259 0.6851725 20 rs10004136 STX18 4 4463587 0.5296092 21 rs10004516 ENPEP 4 111398208 0.8564897 22 rs1000521 SLC8A3 14 70522484 0.6234326 23 rs10005849 DCHS2 4 155287317 0.8192577 24 rs10006362 RGS12 4 3319271 0.8061674 25 rs1000640 WWP2 6 69905668 0.2682735 26 rs10006580 PCDH18 4 138449812 0.5178650 27 rs10006676 CYTL1 4 5021086 0.3531493 28 rs10006845 PCDH7 4 31116375 0.4817453 29 rs10007075 NEIL3 4 178274694 0.5433481 31 rs10008636 TMPRSS11BNL 4 69083563 0.8346434 32 rs10008910 UBA6 4 68500171 0.5705853 33 rs10009228 CHRNA9 4 40356422 0.4223378 rare: geneName txStart txEnd Chrom position p 36131 YTHDC1 6026 45746 4 6026 0.5009490 10898 FAM110C 38813 46588 19 38813 1.0000000 37306 ZNF595 53178 88099 4 53178 0.1261045 16450 KIR2DL4 57208 68123 19 57208 0.0000156 28406 SCAND3 61610 77316 6 61610 0.2568 19926 MPG 127017 135850 6 127017 00.000987456 34149 TRIM27 174179 195169 6 174179 0.025698 I haven't included all information here. Any help will be greatly appreciated. Thanks! ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.