[R] Font size in geom_dl (using ggplot2)
John Kane
jrkrideau at inbox.com
Fri Aug 31 20:59:13 CEST 2012
HI Mathias,
We were all beginners recently. You only replied to me. It is a good idea to do a reply all so that the many readers of r-help at r-project.org get a chance to read it. Most of them are a lot more expert than I am. I have reposted this response to the list.
First: dput() is a function to output a data set in an easy-to-read format in email, etc.
Your data is in "m" so you simply do : dput(m) and you will get the result I have added a bit later. One cimply copies and pastes the resulting output into the email.
So far I have gotten nowhere with your problem. It looks to me as if your code should work although I see a few references to using cex rather than size if you use direct.label rather than the newer geom_dl but if it works I cannot get it to.
I have cut down your example to have just the key elements of the problem. Most of the formatting, etc., in the code is superfluous to the problem as far as I can see. In case I am wrong I have appended your original code below the data set for others to check.
Here is the amended code:
#=========================================================#
library(ggplot2)
library(reshape2)
library(grid)
library(directlabels)
#
# m <- read.csv("/home/john/rdata/dilsample.txt",, sep ="\t", header = TRUE)
# get dput form of data below
m_sig <- m[m$sig == "+" & m$dif > 0, ]
p <- ggplot() +
opts(legend.position="none") +
geom_point(data=m, aes(x=dif, y=pvalue, colour=sig), shape=19, cex=6, alpha=0.3)
p # looks fine so far.
p1 <- p +geom_dl(method="top.bumptwice", data=m_sig,
aes(x=dif, y=pvalue, label=gene.name, colour=sig), size=20)
p1 # oops no change in text size.
#==================data set=================================#
m <- structure(list(protein.ID = structure(1:668, .Label = c("A2A5S3",
"A2A7S7;Q91WQ3", "A2AEX6;A2AEX8;P97447;A2AEY2;A2AEY1;A2AEX7;P97447-2;A2AEY0",
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359L, 360L, 361L, 362L, 363L, 364L, 365L, 366L, 367L, 368L, 369L,
370L, 371L, 372L, 373L, 374L, 375L, 376L, 377L, 378L, 379L, 380L,
381L, 382L, 383L, 384L, 385L, 386L, 387L, 388L, 389L, 390L, 391L,
392L, 393L, 394L, 395L, 396L, 397L, 398L, 399L, 400L, 401L, 402L,
403L, 404L, 405L, 406L, 407L, 408L, 409L, 410L, 411L, 412L, 413L,
414L, 415L, 416L, 417L, 418L, 419L, 420L, 421L, 422L, 423L, 424L,
425L, 426L, 427L, 428L, 429L, 430L, 431L, 432L, 433L, 434L, 435L,
436L, 437L, 438L, 439L, 440L, 441L, 442L, 443L, 444L, 445L, 446L,
447L, 448L, 449L, 450L, 451L, 452L, 453L, 454L, 455L, 456L, 457L,
458L, 459L, 460L, 461L, 462L, 463L, 464L, 465L, 466L, 467L, 468L,
469L, 470L, 471L, 472L, 473L, 474L, 475L, 476L, 477L, 478L, 479L,
480L, 481L, 482L, 483L, 484L, 485L, 486L, 487L, 488L, 489L, 490L,
491L, 492L, 493L, 494L, 495L, 496L, 497L, 498L, 499L, 500L, 501L,
502L, 503L, 504L, 505L, 506L, 507L, 508L, 509L, 510L, 511L, 512L,
513L, 514L, 515L, 516L, 517L, 518L, 519L, 520L, 521L, 522L, 523L,
524L, 525L, 526L, 527L, 528L, 529L, 530L, 531L, 532L, 533L, 534L,
535L, 536L, 537L, 538L, 539L, 540L, 541L, 542L, 543L, 544L, 545L,
546L, 547L, 548L, 549L, 550L, 551L, 552L, 553L, 554L, 555L, 556L,
557L, 558L, 559L, 560L, 561L, 562L, 563L, 564L, 565L, 566L, 567L,
568L, 569L, 570L, 571L, 572L, 573L, 574L, 575L, 576L, 577L, 578L,
579L, 580L, 581L, 582L, 583L, 584L, 585L, 586L, 587L, 588L, 589L,
590L, 591L, 592L, 593L, 594L, 595L, 596L, 597L, 598L, 599L, 600L,
601L, 602L, 603L, 604L, 605L, 606L, 607L, 608L, 609L, 610L, 611L,
612L, 613L, 614L, 615L, 616L, 617L, 618L, 619L, 620L, 621L, 622L,
623L, 624L, 625L, 626L, 627L, 628L, 629L, 630L, 631L, 632L, 633L,
634L, 635L, 636L, 637L, 638L, 639L, 640L, 641L, 642L, 643L, 644L,
645L, 646L, 647L, 648L, 649L, 650L, 651L, 652L, 653L, 654L, 655L,
656L, 657L, 658L, 659L, 660L, 661L, 662L, 663L, 664L, 665L, 666L,
1L, 1L, 1L), .Label = c("", "1200014J11Rik", "2310008H09Rik",
"Abcf1", "Abi3bp", "Acacb", "Acin1", "Acta2", "Actg1", "Adar",
"Adarb1", "Aebp1", "Ahnak", "Ahnak2", "Aimp1", "Akap8", "Alyref",
"Anxa1", "Apc2", "Arglu1", "Arhgef2", "Arhgef40", "Asph", "Atp5a1",
"BC006779", "Bclaf1", "Bub3", "Cald1", "Calm1", "Caprin1", "Capza2",
"Carm1", "Ccar1", "Ccdc86", "Ccnk", "Cd3eap", "Cdc42", "Cdc5l",
"Cdk12", "Cdk13", "Cdk9", "Cdkn2aip", "Cdkn2aipnl", "Cep170",
"Cfl1", "Chd3", "Cherp", "Cirbp", "Ckap4", "Clasp1", "Clasp2",
"Clip2", "Clk3", "Clp1", "Cnbp", "Cnn3", "Cobra1", "Copa", "Copb2",
"Cope", "Cpsf1", "Cpsf2", "Cpsf3", "Cpsf4", "Cpsf6", "Cpsf7",
"Csda", "Csde1", "Cstf1", "Cstf2", "Cstf2t", "Cstf3", "Ctcf",
"Cttn", "Cyfip1", "D10Wsu52e", "D2Wsu81e", "D8Ertd738e", "Dars",
"Ddx1", "Ddx17", "Ddx18", "Ddx20", "Ddx21", "Ddx23", "Ddx24",
"Ddx3x", "Ddx3y", "Ddx42", "Ddx46", "Ddx47", "Ddx5", "Ddx50",
"Ddx52", "Ddx55", "Ddx56", "Ddx58", "Dgcr8", "Dhrs4", "Dhx15",
"Dhx30", "Dhx36", "Dhx37", "Dhx58", "Dhx9", "Dicer1", "Dkc1",
"Dnaja1", "Dnaja2", "Dnajc10", "Dnajc9", "Dnmt1", "Dpy30", "Drg1",
"Drosha", "Dsp", "Dstn", "Dus3l", "Dzip3", "Eef1a1", "Eef1d",
"Eef2", "Eefsec", "Eftud2", "Eif2ak2", "Eif3h", "Eif4e", "Eif4enif1",
"Eif4g1", "Eif4g3", "Eif5a", "Elavl1", "Epb4.1l2", "Epb4.1l3",
"Eprs", "Erh", "Eri1", "FAM120A", "Fam120c", "Fam164a", "Fam207a",
"Fam98b", "Farp1", "Farsa", "Farsb", "Fau", "Fbl", "Fbln2", "Fhl1",
"Fhl2", "Fhl3", "Fip1l1", "Fiz1", "Flna", "Fmr1", "Fn1", "Frg1",
"Ftsjd1", "Ftsjd2", "Fubp3", "Fxr1", "G3bp1", "G3bp2", "Gar1",
"Gemin2", "Gemin4", "Gemin5", "Gemin6", "Gemin7", "Gemin8", "Gle1",
"Glyr1", "Gm10036", "Gm10093", "Gm10094", "Gm10119", "Gm10154",
"Gm10260", "Gm10774", "Gm13646", "Gm14446", "Gm2606", "Gm4294",
"Gm4963", "Gm6793", "Gm7935", "Gnb2l1", "Gnl2", "Gnl3", "Grsf1",
"Grwd1", "Gsn", "Gtpbp1", "H1f0", "H1fx", "Hdlbp", "Hexim1",
"Hist1h1a", "Hist1h1b", "Hist1h1c", "Hist1h1d", "Hist1h1e", "Hist1h2ab",
"Hist1h3b", "Hist1h4a", "Hist2h2aa1", "Hmga2", "Hmmr", "Hnrnpa0",
"Hnrnpa1", "Hnrnpa2b1", "Hnrnpab", "Hnrnpc", "Hnrnpd", "Hnrnpf",
"Hnrnph1", "Hnrnph2", "Hnrnpk", "Hnrnpl", "Hnrnpm", "Hnrnpr",
"Hnrnpu", "Hnrnpul1", "Hnrnpul2", "Hnrpdl", "Hnrpll", "Hp1bp3",
"Hsd17b12", "Hsp90ab1", "Hspa1b", "Hspa5", "Hspa8", "Hspa9",
"Hspd1", "Iars", "Ifih1", "Ifit1", "Ifitm3", "Igf2bp1", "Igf2bp2",
"Igf2bp3", "Ilf2", "Ilf3", "Ints3", "Iqgap1", "Isg20l2", "Jup",
"Kars", "Khdrbs1", "Khsrp", "Kif14", "Kif1c", "Kif2a", "Kpna2",
"Kpna3", "Kpna4", "Kpnb1", "Ktn1", "Larp7", "Ldha", "Lgals1",
"Lgals3bp", "Lima1", "Lmna", "Lrrc59", "Lsm14a", "Lsm14b", "Lsm2",
"Lsm3", "Lsm4", "Lsm5", "Lsm6", "Lsm7", "Luc7l", "Luc7l2", "Luc7l3",
"Lyar", "Map1b", "Map4", "Map7d1", "Mark3", "Mars", "Matr3",
"Mbnl1", "Mccc1", "Mccc2", "Mepce", "Metap1", "Mina", "Mki67ip",
"Mkrn2", "Morf4l2", "Mov10", "Mrpl3", "Mtap", "Mtap1a", "Mvp",
"Mybbp1a", "Myef2", "Myh10", "Myh14", "Myh9", "Myl12a", "Myl6",
"Myo1c", "Myo9b", "Naa38", "Nars", "Ncbp1", "Ncbp2", "Ncl", "Neil1",
"Nemf", "Nfix", "Nhp2l1", "Nono", "Nop2", "Nop56", "Nop58", "Npm1",
"Nsun2", "Nsun5", "Nudt21", "Nufip1", "Nufip2", "Numa1", "Nupl2",
"Nxf1", "Nxt1", "Oas3", "Oasl2", "P4ha1", "P4hb", "Pabpc1", "Pabpc4",
"Pabpn1", "Parp1", "Parp12", "Pcbp1", "Pcbp2", "Pcca", "Pccb",
"Pcf11", "Pcx", "Pdcd11", "Pdcd7", "Pes1", "Pgam5", "Phax", "Phf5a",
"Phf6", "Pip5k1a", "Pkm2", "Plec", "Plk1", "Plod1", "Pnn", "Poldip3",
"Polr1c", "Polr1e", "Polr2a", "Polr2b", "Polr2e", "Polr2h", "Polr3a",
"Polr3b", "Polr3c", "Polr3d", "Polr3e", "Polr3f", "Polr3k", "Pop1",
"Ppih", "Ppp1cb", "Prc1", "Prdx1", "Prkcdbp", "Prkra", "Prmt1",
"Prpf19", "Prpf3", "Prpf31", "Prpf38b", "Prpf4", "Prpf40a", "Prpf4b",
"Prpf6", "Prpf8", "Prrc2a", "Prrc2c", "Prrx1", "Psip1", "Pspc1",
"Ptbp1", "Ptn", "Ptrf", "Puf60", "Purb", "Raly", "Ran", "Ranbp1",
"Rars", "Rbbp4", "Rbm14", "Rbm15", "Rbm17", "Rbm19", "Rbm25",
"Rbm26", "Rbm27", "Rbm3", "Rbm39", "Rbm42", "Rbm7", "Rbms1",
"Rbms2", "Rbmxl1", "Rcc2", "Rdbp", "Reep4", "Rexo4", "Rfc1",
"Rfc2", "Rfc3", "Rfc4", "Rfc5", "Rnf213", "Rnh1", "Rnmt", "Rnpc3",
"Rnps1", "Rpl10", "Rpl10a", "Rpl12", "Rpl13", "Rpl13a", "Rpl14",
"Rpl17-ps3", "Rpl18", "Rpl18a", "Rpl19", "Rpl21", "Rpl22", "Rpl22l1",
"Rpl23", "Rpl23a", "Rpl24", "Rpl26", "Rpl27", "Rpl27a", "Rpl28",
"Rpl29", "Rpl3", "Rpl30", "Rpl31", "Rpl32", "Rpl35", "Rpl36a",
"Rpl36-ps3", "Rpl37a", "Rpl38", "Rpl39", "Rpl4", "Rpl6", "Rpl7",
"Rpl7a", "Rpl8", "Rpl9", "Rplp0", "Rplp2", "Rpn1", "Rps11", "Rps12",
"Rps13", "Rps14", "Rps15", "Rps15a", "Rps16", "Rps17", "Rps19",
"Rps2", "Rps20", "Rps21", "Rps23", "Rps24", "Rps26", "Rps27",
"Rps27a", "Rps28", "Rps29", "Rps3", "Rps4x", "Rps5", "Rps6",
"Rps7", "Rps8", "Rps9", "Rpsa", "Rrbp1", "Rrp12", "Rrp1b", "Rsbn1",
"Rsbn1l", "Rsl1d1", "Rtp4", "Ruvbl1", "Ruvbl2", "S100a4", "S100a6",
"Samhd1", "Sart1", "Sart3", "Scaf1", "Scaf11", "Sdpr", "Serbp1",
"Serpinh1", "Sf1", "Sf3a1", "Sf3a2", "Sf3a3", "Sf3b1", "Sf3b14",
"Sf3b2", "Sf3b3", "Sf3b5", "Sfpq", "Sgpl1", "Skiv2l2", "Slc25a5",
"Slit2", "Sltm", "Smarca5", "Smc4", "Smn1", "Smndc1", "Snrnp200",
"Snrnp40", "Snrnp48", "Snrnp70", "Snrpa1", "Snrpc", "Snrpd1",
"Snrpd2", "Snrpd3", "Snrpe", "Snrpf", "Snrpn", "Son", "Spats2",
"Spats2l", "Srbd1", "Srek1", "Srfbp1", "Srp19", "Srpk1", "Srpk2",
"Srrm1", "Srrm2", "Srrt", "Srsf1", "Srsf10", "Srsf11", "Srsf2",
"Srsf3", "Srsf4", "Srsf5", "Srsf6", "Srsf7", "Srsf9", "Ssb",
"Ssbip1", "Stau1", "Strap", "Strbp", "Sugp1", "Sulf1", "Supt16h",
"Surf6", "Syncrip", "Tarbp2", "Tardbp", "Tceb1", "Tceb3", "Tcof1",
"Tecr", "Tfam", "Tfb1m", "Th1l", "Thap4", "Thrap3", "Tia1", "Tial1",
"Timm8b", "Tmod3", "Tmpo", "Toe1", "Top1", "Tpi1", "Tpm1", "Tpm3",
"Tpm4", "Tpp1", "Tra2a", "Tra2b", "Trim25", "Trim28", "Trim3",
"Trim56", "Trip12", "Trmt1l", "Trmt2a", "Trp53", "Tsn", "Tsnax",
"Tubb4b", "Tubb5", "Tubb6", "Txn", "U2af1", "U2af1l4", "U2af2",
"U2surp", "Ubtf", "Vim", "Wdr33", "Wdr46", "Wdr6", "Whsc1", "Whsc2",
"Xab2", "Xrn1", "Xrn2", "Yars", "Ybx1", "Ywhag", "Ywhah", "Ywhaq",
"Ywhaz", "Zbtb7a", "Zc3h10", "Zc3h11a", "Zc3h15", "Zc3h18", "Zc3h7b",
"Zc3hav1", "Zcchc24", "Zcchc4", "Zcchc6", "Zcchc8", "Zcrb1",
"Zfc3h1", "Zfp187", "Zfp281", "Zfp346", "Zfp385a", "Zfr", "Zmat3",
"Znf48", "Znf629", "Znf771", "Znf787", "Znfx1", "Znhit3", "Znhit6",
"Zrsr2"), class = "factor"), sig = structure(c(1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 1L,
2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L), .Label = c("", "+"), class = "factor"),
pvalue = c(0.75348473, 0.159767704, 0.062825198, 0.52190158,
0.536177871, 0.041039855, 0.702233817, 1.64242698, 0.580648666,
0.003797673, 0.448358122, 0.733545207, 0.308591344, 0.21997468,
0.032461996, 0.031836341, 0.139860394, 0.039216967, 0.031042867,
0.10870769, 0.020249938, 0.109770721, 0.04692276, 0.545049051,
0.66526319, 0.117900508, 0.291715464, 0.127610506, 0.273426839,
0.404548622, 0.200021897, 0.317507138, 0.015619314, 1.013332349,
1.876113856, 0.443847794, 1.332949198, 0.025591796, 0.5289315,
0.11339967, 0.09287556, 0.991094044, 0.646165723, 0.382552246,
0.167232632, 0.218431902, 0.127158043, 1.878242611, 0.187534817,
0.034790884, 0.29833747, 0.470329625, 0.442527806, 0.203023529,
1.117745884, 0.386849862, 0.22631924, 0.532887126, 0.019501836,
0.354621718, 0.138283313, 0.578753757, 0.399641839, 0.145207112,
0.804629729, 0.352661242, 0.907274233, 0.40553271, 0.26627601,
0.18046599, 0.0047299, 0.066134864, 0.07646334, 0.765758033,
0.092703258, 0.349363906, 1.560827179, 0.075335777, 0.117250418,
0.584489406, 0.657343384, 0.941127255, 0.423120904, 0.075788631,
0.161853173, 0.06511113, 0.216137512, 0.164392256, 0.425298949,
0.099886489, 2.026562029, 0.462464814, 0.153194053, 0.018815394,
0.398729029, 0.309673304, 0.026669416, 0.064101488, 1.257594808,
0.239468116, 2.225401914, 0.554285625, 0.265022568, 0.72481667,
0.263244069, 0.880748106, 0.356951496, 1.428439437, 0.517278136,
0.047373535, 0.789208209, 1.010248109, 1.771834903, 0.132359176,
0.082919202, 0.918589566, 0.588323983, 0.210377833, 0.469248749,
1.02299174, 0.052209049, 0.002555547, 1.923366795, 0.174133031,
0.577521065, 0.833608225, 0.053891755, 0.493901676, 0.194946721,
0.072651594, 0.27380698, 0.427159406, 0.125008048, 0.002361555,
0.553941939, 0.125323397, 0.371570151, 0.459609537, 0.08773595,
0.08205066, 1.360805758, 0.128275548, 0.035167213, 0.496001347,
3.108969193, 0.625492424, 0.166056986, 0.156562158, 0.250755458,
0.193889935, 0.041776963, 0.01314011, 1.647580224, 1.219229859,
0.291631718, 0.565760786, 0.485222574, 0.97026749, 0.822848832,
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-1.623640696, 0.280188243, -0.605463664, -0.233766556, 3.682554881,
-0.547206243, -0.450004578, 0.034355164, 0.16519165, -0.090838114,
-0.711037318, -0.191608429, 0.026894252, -0.290318171, -0.160797755,
-0.024990718, 0.888919512, -1.597884496, 0.314945857, 0.059834798,
0.106431325, 0.25725174, -0.111471812, -0.214009603, 0.658617655,
-0.208488464, -0.20691363, 0.330897013, -0.861095746, 0.143809001,
-0.016296387, 0.090005239, -0.202548345, 0.089533488, 0.181583405,
-0.04567337, -1.016190529, -0.060263316, 0.051520665, -0.067797343,
0.182441711, 0.588282267, 0.389160156, -0.369526545, 0.254364014,
-0.148995717, -1.046162287, -0.112155279, -0.795994123, -0.170350393,
-0.054634094, -1.653266271, -0.17369779, 0.504775365, 0.052454631,
0.209945679, -0.073120753, 0.148504893, 2.691055616, -0.463953018,
0.06917572, -0.151784261, -0.119426092, 0.159910202, -0.387921651,
0.214939753, -0.031418482, -0.268153826, 0.363521576, -0.395782153,
-0.348925908, -0.632455508, -0.124678294, 0.393573125, 0.268884023,
0.321352641, -0.436938604, 0.150749842, -0.070432663, -0.270679474,
0.022648493, 0.029236476, -0.747723897, 0.994194031, -0.678286552,
0.425589244, -0.517005285, -1.043352763, -0.161347389, -0.061066945,
-0.087617238, 0.155469259, 0.508115768, 0.302708308, 0.407255809,
0.612781525, 0.275043488, -0.214604696, 0.031771342, -0.069987615,
0.011262894, 0.010667801)), .Names = c("protein.ID", "gene.name",
"sig", "pvalue", "dif"), class = "data.frame", row.names = c(NA,
-668L))
#============================Original code===================#
library(ggplot2)
library(reshape2)
library(grid)
library(directlabels)
theme_complete_bw <- function(base_size = 15) {
structure(list(
axis.line = theme_segment(size = base_size*0.1),
axis.text.x = theme_text(size = base_size*1.3, lineheight = 0.9, colour = "gray10"),
axis.text.y = theme_text(size = base_size*1.3, lineheight = 0.9, colour = "gray10"),
axis.ticks = theme_segment(colour = "black", size = base_size*0.1),
axis.title.x = theme_text(size = base_size*1.5, vjust=-0.25),
axis.title.y = theme_text(size = base_size*1.5, angle = 90, vjust = 0.25),
axis.ticks.length = unit(0.15, "cm"),
axis.ticks.margin = unit(0.15, "cm"),
panel.background = theme_blank(),
panel.border = theme_blank(),
panel.grid.major = theme_blank(),
panel.grid.minor = theme_blank(),
panel.margin = unit(0.25, "lines"),
strip.background = theme_rect(fill = NA, colour = NA),
strip.text.x = theme_text(colour = "black", size = base_size * 0.8),
strip.text.y = theme_text(colour = "black", size = base_size * 0.8, angle = -90),
plot.background = theme_rect(colour = NA, fill = "white"),
plot.title = theme_text(size = base_size * 2, face="bold"),
plot.margin = unit(c(0.5, 1, 0.5, 0.5), "lines")
), class = "options")
}
cols <- c("royalblue4", "firebrick3")
m <- read.table("sample.txt", sep="\t", header=T)
m_sig <- m[m$sig == "+" & m$dif > 0, ]
ggplot()+
opts(legend.position="none")+
xlab("log2 fold change")+ ylab("-log10 P value")+
xlim(-15,15) + ylim(0,6)+
theme_complete_bw()+
scale_colour_manual(values=cols)+
geom_point(data=m, aes(x=dif, y=pvalue, colour=sig), shape=19, cex=6, alpha=0.3)+
geom_dl(method="top.bumptwice", data=m_sig, aes(x=dif, y=pvalue, label=gene.name, colour=sig), size=20)
John Kane
Kingston ON Canada
> -----Original Message-----
> From: mhabjan at gmx.at
> Sent: Thu, 30 Aug 2012 23:17:28 +0200
> To: jrkrideau at inbox.com
> Subject: AW: [R] Font size in geom_dl (using ggplot2)
>
> Dear John,
>
> thank you for your immediate reply
and sorry for the beginner’s mistakes
> ;)
> Unfortunately it took a while to put the data in an email-compatible
> format.
> Didn't get the dput() function - yes I'm really that of a beginner...
>
> BUT: I attached a sample table (samplex.txt), the full code (R_Code.txt),
> and the version infos (sessionInfo.txt).
>
> Hope that you can replicate the problem and I would very much appreciate
> if
> you could help me out on this one.
>
> Thanks a lot,
> Matthias
>
> -----Ursprüngliche Nachricht-----
> Von: John Kane [mailto:jrkrideau at inbox.com]
> Gesendet: Dienstag, 28. August 2012 21:26
> An: Matthias Habjan; r-help at r-project.org
> Betreff: RE: [R] Font size in geom_dl (using ggplot2)
>
> Sample data? Some representative sample data really is needed to see
> what
> you are doing. Have a look at dput() for a handy way to present data.
>
> Also where did theme_complete_bw come from? Is it a special formattng
> function?
>
> John Kane
> Kingston ON Canada
>
>
>> -----Original Message-----
>> From: mhabjan at gmx.at
>> Sent: Tue, 28 Aug 2012 00:14:20 +0200
>> To: r-help at r-project.org
>> Subject: [R] Font size in geom_dl (using ggplot2)
>>
>> Hey everyone,
>>
>> I am an R-newby... so sorry for bothering you with simple-to-solve
>> questions;) I have the following issue: trying to add labels to my
>> scatterplots (with geom_dl in ggplot2). Everything works fine, but
>> after checking every resource I do not find a way to change the font
>> size of my labels. I tried size, cex, fontsize at every position...
>> but it always stays the same.
>>
>> ggplot()+
>> opts(legend.position="none")+
>> xlab("x")+ ylab("y")+
>> xlim(-15,15) + ylim(0,6)+
>> theme_complete_bw()+
>> scale_colour_manual(values=cols)+
>> geom_point(data=m, aes(x=x, y=y, colour=s), shape=19, cex=6,
>> alpha=0.3)+
>> geom_dl(method="top.bumptwice", data=m_sig, aes(x=x, y=y,
>> label=gene.name, colour=s, size=10))+
>> geom_line(data=m_s0, aes(x= x, y=y), linetype=5, colour="grey55",
>> size=0.5)
>>
>> Your help is very much appreciated! Thx.
>>
>> ______________________________________________
>> R-help at 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.
>
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