[R] Font size in geom_dl (using ggplot2)

John Kane
2012-08-31T18:59:13Z

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",
"A2AH85;O08810;G3UZ34;G3UXK8;G3UZ25",
"A2AJI0;A8Y5P4;A2AJI0-2;A2AJI1;F6WF36",
"A2ARP8;Q9QYR6-2;Q9QYR6",
"A2AS03;E9QAM5;A2AS05;E9Q8D9;E9Q7J7",
"A2AWT5;P25976;A2AWT7;A2AWT6;P25976-2;E9Q4A8",
"A2RSY6;A2RSY6-2;A2RSY6-3;A2RSY6-4",
"A6H6N4;F2Z455;Q9R059;D6RJ68",
"B1AR17;E9Q614;F7C528;E9PYL1;A2A8L1;E9PYU4;F6SLC9;F6WR45;F6V4V3",
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"B2RVL6", "B2RXC6",
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238L, 239L, 240L, 241L, 242L, 243L, 244L, 245L, 246L, 247L, 248L,
249L, 250L, 251L, 252L, 253L, 254L, 255L, 256L, 257L, 258L, 259L,
260L, 261L, 262L, 263L, 264L, 265L, 266L, 267L, 268L, 269L, 270L,
271L, 272L, 273L, 274L, 275L, 276L, 277L, 278L, 279L, 280L, 281L,
282L, 283L, 284L, 285L, 286L, 287L, 288L, 289L, 290L, 291L, 292L,
293L, 294L, 295L, 296L, 297L, 298L, 299L, 300L, 301L, 302L, 303L,
304L, 305L, 306L, 307L, 308L, 309L, 310L, 311L, 312L, 313L, 314L,
315L, 316L, 317L, 318L, 319L, 320L, 321L, 322L, 323L, 324L, 325L,
326L, 327L, 328L, 329L, 330L, 331L, 332L, 333L, 334L, 335L, 336L,
337L, 338L, 339L, 340L, 341L, 342L, 343L, 344L, 345L, 346L, 347L,
348L, 349L, 350L, 351L, 352L, 353L, 354L, 355L, 356L, 357L, 358L,
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,
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    -0.255764325, -0.453524272, 0.011152903, -0.333488464, 0.407763799,
    0.29241689, -0.529022217, -0.05754598, -0.627913157, 0.407667796,
    0.182380676, -0.051679611, 0.0584596, 0.207442602, -0.116637548,
    0.083866755, -0.332674662, 0.031808217, -0.766137441, 0.523780187,
    0.526952744, 0.067832947, 0.371782303, 0.123615901, -0.02991422,
    0.214763641, -5.195489883, -0.025772095, 0.788716634, 4.638476054,
    -0.159856796, -0.705746333, 0.528317769, 1.598258972, 0.324183146,
    0.12885348, -0.031502406, 0.351457596, 0.485436757, 0.136620204,
    0.03565979, 0.099957148, -0.42109553, -1.748673121, 0.122387568,
    -0.142484665, 0.132631938, 1.30876414, -0.390500387, 0.464392344,
    -0.105558395, 0.095080058, 0.480608622, -0.328005473, -1.138511658,
    0.186700821, -1.637097677, 0.142434438, 0.206543605, -0.093142827,
    0.858149846, 0.144253413, 0.177417119, -1.660070101, -0.277237574,
    -0.250320435, -1.702219009, -0.178300222, -0.162923177, -0.477787336,
    -0.09006691, -0.037643433, -0.293295542, 0.183410645, 0.10966301,
    -0.287601471, -0.184579213, -0.052760442, 0.0796477, 0.167708715,
    -0.151818593, -0.879341125, 0.14475441, 0.231157939, -0.22473526,
    0.184297562, 0.112517039, -1.132635752, -0.400759379, 0.074510574,
    -0.202440262, 0.169664383, 0.376533508, -0.01207606, -0.308247248,
    -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
>
> -----Urspr?ngliche 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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