A New Interface to Render Graphs Using Rgraphviz
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1 A Nw Intr to Rnr Grps Usn Rrpvz Florn Hn Otor 30, 2017 Contnts 1 Ovrvw 1 2 Introuton 1 3 Dult rnrn prmtrs Dult no prmtrs Dult prmtrs Dult rpw prmtrs Prmtrs or nvul nos/s 10 5 Grpl prmtrs tt t t lyout No sps E rrows n rrowtls Sssonno 19 1 Ovrvw Ts vntt sows ow to us Rrpvz s upt ntr or rnrn o rps. For tls on rp lyout s t Vntt How To Plot A Grp Usn Rrpvz. Not tt t sn o t ntr s npnnt o rpvz, owvr no nns to ny otr rp lyout sotwr v n mplmnt so r. 2 Introuton Tr r two stnt prosss wn plottn rps: lyout, w pls nos n s n (usully two-mnsonl) sp, n rnrn, w s t tul rwn o t rp on rps v. T rst pross 1
2 s typlly t mor omputtonlly xpnsv on n rls on sopstt lortms tt rrn t rp s omponnts s on rnt rtr. T rrnmnt o t nos n s pns on vrous prmtrs su s t sr no sz, w n my unton o t sz o t no lls. Rnrn o rp s otn sut to rqunt ns n ptons, n t mks sns to sprt t two prosss n t sotwr mplmntton. It s lso mportnt to rlz tt t pross o ttn oo lyout s trtv, n usn ult prmtr sttns slom yls oo plots. T o vll or on rp lyout n Boonutor s s mnly on t Grpvz prot n t Boost rp lrry. Howvr, us t rnrn o rp s sprt rom t lyout, on n us otr rp lyout lortms, s lon s t rqurmnts o t rnrn ntr r mt. In t pross o lyn out rp som mount o normton s nrt, mostly rrn t lotons n mnsons o nos on two-mnsonl pln n t trtors o t s. Boonutor rp ots now ontn slot rnrino to ol ts normton. T typl worklow o rp lyout s to pss rp ot to t lyout unton, w rturns notr rp ot ontnn ll t nssry normton or susqunt rnrn. T pross o lln lyout lortm s npsult n t lyoutgrp unton. Clln ts unton wtout ny urtr rumnts wll rsult n usn on o t Grpvz lyout lortms v t t Rrpvz pk. W ssum knowl o rp lyout n t vll Grpvz optons n t rmnr o ts Vntt n wll mostly l wt t rnrn prt, r. T rnrn o rp rls solly on R s ntrnl plottn plts. As or ll otr plottn untons n R, mny prmtrs ontrolln t rpl output n tun. Howvr, us tr r svrl prts o rp on mt wnt to moy (.., nos, s, ptons), sttn t rpl prmtrs s sltly mor omplx tn or otr plots. W v stls rry to st lol ults, rp-sp prmtrs, n sttns tt pply only to nvul rnrn oprtons. To monstrt t nw rnrn ntr w rst nrt rp usn t rp pk n ly t out usn t ult Grpvz ot lyout. > lrry("rrpvz") > st.s(123) > V <- lttrs[1:10] > M <- 1:4 > 1 <- rnomgrp(v, M, 0.2) > 1 <- lyoutgrp(1) > rnrgrp(1) 2
3 3 Dult rnrn prmtrs Tr s rry to st rnrn prmtrs or rp. T lvls o ts rry r 1. T ssson: Ts r t ults tt wll us or prmtr not st somwr urtr own t rry. You n n t ssson ults t ny tm usn t unton rp.pr. 2. Rnrn oprton: Dults n st or snl rnrn oprton, tt s, or snl ll to rnrgrp usn ts rp.prs rumnt. 3. Invul nos or s: Prmtrs or nvul nos or s n rp ot n st usn t nornrino n RnrIno untons. Not tt ll prmtrs st n rnrgrp s rp.prs rumnt r trnsnt, wrs sttn ssson-w prmtrs wll t ll susqunt rnrn oprtons. Sttn prmtrs v t nornrino n RnrIno untons ts t nvul rp ots, n ts ns wll ovously rtn n ll susqunt lyout or rnrn oprtons o tt prtulr rp. 3
4 3.1 Dult no prmtrs W now us our xmpl rp to urtr xplor ts optons. Lt s strt wt t nos: W wnt to ll ll our nos wt ry olor n us r olor or t no nms. Sn ts soul ppl to ll nos, w st lol rnrn prmtr usn rp.pr: > rp.pr(lst(nos=lst(ll="ltry", txtcol="r"))) > rnrgrp(1) Sttn ssson-w prmtr s s-ts or ll susqunt rnrn oprtons, n w wll soon s ow to rv t sm sttn usn t nornrino unton. Not tt rp.pr tks s snl rumnt lst o rnrn prmtrs. Tr r tr rnt typs o prmtrs t usr mt wnt to st: now prmtrs, w prmtrs n prmtrs tt ontrol turs o t wol rp. Aornly, t prmtrs lst pss to rp.pr my ontn t lst tms nos, s n rp. E o ts lst tms n n lst o vll plottn prmtrs. In our xmpl, t prmtrs r ll n txtcol. All urrntly vll no prmtrs r: ˆ ol: t olor o t ln rwn s no orr. Dults to lk. ˆ lty: t typ o t ln rwn s no orr. Dults to sol. Vl vlus r t sm s or t R s s rp prmtr lty. 4
5 ˆ lw: t wt o t ln rwn s no orr. Dults to 1.Not tt t unrlyn low lvl plottn untons o not support vtorz lw vlus. Inst, only t rst tm o t vtor wll us. ˆ ll: t olor us to ll no. Dults to trnsprnt. ˆ txtcol:t ont olor us or t no lls. Dults to lk. ˆ ontsz: t ont sz or t no lls n ponts. Dults to 14. Not tt t ontsz wll utomtlly ust to mk sur tt ll lls t tr rsptv nos. You my wnt to nrs t no sz y supplyn t pproprt lyout prmtrs to Grpvz n orr to llow or lrr ontszs. ˆ x: Expnson tor to urtr ontrol t ontsz. As ult, ts prmtr s not st, n w s t ontsz wll lpp to t no sz. Ts mnly xsts to or onsstny wt t s rp prmtrs n to ovrr t lppn o ontsz to nosz. ˆ sp: Ts s not rlly rpl prmtr. S Ston 5 or tls. In t nxt o unk w st t ults or ll rmnn no prmtrs: > rp.pr(lst(nos=lst(ol="rkrn", lty="ott", lw=2, ontsz=6))) > rnrgrp(1) 5
6 Smlr to R s s pr unton, t ornl vlus o mo prmtr r rturn y rp.pr n you my wnt to ssn tm to n ot n orr to ltr rvrt your ns. A usul tur wn plottn rps s to ontrol t sp o t nos. Howvr, sps v n mpt on t l loton o nos n, vn mor so, t s twn tm. Hn, t lyout lortm ns to r-run wnvr tr r ns n no sps. In Ston 5 w wll lrn ow to ontrol no sps n lso som turs o t s. 3.2 Dult prmtrs Now, lt s tk look t t prmtrs tt ontrol t pprn o s. Ty r: ˆ ol: t olor o t ln. Dults to lk. ˆ lty: t typ o t ln. Dults to sol. Vl vlus r t sm s or t R s s rp prmtr lty. ˆ lw: t wt o t ln. Dults to 1. ˆ txtcol:t ont olor us or t lls. Dults to lk. ˆ ontsz: t ont sz or t lls n ponts. Dults to 14. ˆ x: Expnson tor to urtr ontrol t ontsz. Ts mnly xsts to onsstnt wt t s rp prmtrs. ˆ rrow, rrowtl An, not rlly plottn prmtr. Ston 5 provs tls. Frst, w st som ttruts tt ontrol t lns. > rp.pr(lst(s=lst(ol="ltlu", lty="s", lw=3))) > rnrgrp(1) 6
7 In orr to sow t ts o t ll prmtrs, w rst v to su lls. lyoutgrp wll pss tm on to Grpvz wn ty r sp s Attrs: > lls <- Nms(1) > nms(lls) <- lls > 1 <- lyoutgrp(1, Attrs=lst(ll=lls)) > rnrgrp(1) 7
8 ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ Now w n strt twkn tm: > rp.pr(lst(s=lst(ontsz=18, txtcol="rkr"))) > rnrgrp(1) 8
9 ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ 3.3 Dult rpw prmtrs Som turs o rp r not rlly ttruts o tr nos or s. Ty n ontroll trou t rpw rnrn prmtrs: ˆ mn: txt tt s plott s t mn ttl. Unlss st xpltly, no ttl wll plott. ˆ su: txt tt s plott s suttl t t ottom o t rp. Unlss st xpltly, no suttl wll plott. ˆ ol.mn: t ont olor us or t ttl. Dults to lk. ˆ x.mn: Expnson tor or t ontsz us or t ttl. Dults to 1.2 ˆ ol.su: t ont olor us or t suttl. Dults to lk. ˆ x.su: Expnson tor or t ontsz us or t suttl. Dults to 1 Hr, w ot ttl n suttl to t plot. 9
10 > rp.pr(lst(rp=lst(mn="a mn ttl...", + su="... n suttl", x.mn=1.8, + x.su=1.4, ol.su="ry"))) > rnrgrp(1) A mn ttl... ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~... n suttl O ours w oul st ll rp-, no-, n w prmtrs n on snl ll to rp.pr. Inst o nn lol sttns wt rp.pr w oul lso prov lst wt t sm strutur to rnrgrp trou ts rp.prs rumnt. Tos wll only ppl n t rsptv rnrn oprton, wrs optons st usn t unton rp.pr r rtn trouout t wol R ssson. 4 Prmtrs or nvul nos/s In mny ss w on t wnt to lolly n rtn prmtrs or ll nos or s, ut rtr o ts sltvly to lt nvul nos/s or susts tro. To ts n, prmtrs or nvul nos n s n st usn t nornrino n RnrIno untons. Bot nornrino n RnrIno r rplmnt untons tt oprt rtly on t rp ot. For ompltnss, rprnrino s t unton tt n us to ontrol t rp-w ttruts (lk ptons n suttls). Wn you n prmtr n t rp ot ts wll rr on ross 10
11 ll urtr rnrn n lyout oprtons. T sttns m y Rnr- Ino n nornrino tk prn ovr ll otr ult sttns. T prmtrs to st v to vn s nm lsts, wr lst tm n ontn nm vtors or rtn optons. For xmpl, t ollown o sts t ll olor o nos n to yllow. > nornrino(1) <- lst(ll=(="ltyllow", ="ltyllow")) > rnrgrp(1) A mn ttl... ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~... n suttl T nms o t vtors v to mt t no or nms o t rp. No nms r strtorwr (t rsult o lln t unton nos on rp ot), owvr nms r m up o t nms o t onnt nos sprt y ~, t tl symol. An twn nos n woul nm ~. For rt rp ~ s t om to, n ~ s t rom to. For unrt rps t two r quvlnt. Nms rturns t nms o ll s n rp. T ollown o ns t ln typ o t s twn nos n n nos n to sol n tr ln olor to orn. > RnrIno(1) <- lst(lty=("~"="sol", "~"="sol"), + ol=("~"="orn", "~"="orn")) > rnrgrp(1) 11
12 A mn ttl... ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~... n suttl Cns n t rnrn o sp nos or s s otn motvt y rtn lsss or turs ty rprsnt n w on t wnt to st ts mnully ut rtr us prormmt ppro: > snos <- lttrs[1:4] > ll <- rp("ltlu", lnt(snos)) > nms(ll) <- snos > nornrino(1) <- lst(ll=ll) > rnrgrp(1) 12
13 A mn ttl... ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~... n suttl Bot nornrino n RnrIno lso llow to st prmtrs or ll s or nos o t rp t on. T syntx s smpl: nst o nm vtor on n pss slr or vn prmtr. Ts vlu wll tn ssn to ll vll nos or s. > nornrino(1) <- lst(lty=1) > RnrIno(1) <- lst(lty=1, lw=2, ol="ry") > rnrgrp(1) 13
14 A mn ttl... ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~... n suttl T sst wy to st n ttrut k to ts ult (t ssson ult t s n st) s to pss n NULL lst tm v t rsptv sttr unton. > nornrino(1) <- lst(ll=lst(=null, =NULL)) > rnrgrp(1) 14
15 A mn ttl... ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~... n suttl 5 Grpl prmtrs tt t t lyout As mnton or, som rpl prmtrs r somwt on t orr twn rp lyout n rp rnrn. T sp o t no or xmpl os not rstlly t t s loton, owvr t lyout o t s pontn to n rom ts no mt sltly n. Sn mnpultn ts ttruts s rqunt oprton n rp plottn, w to mk tm vll trou t rnrn ntr. 5.1 No sps No sps n st usn t sp prmtr. Currntly, t rnrn unton supports t ollown sp typs: ˆ rl ts s t ult vlu. Crulr nos r not t y ns n wt or t, t lortm wll lwys us qurt ounn ox ˆ llps ts sp llows or rns n wt n t. Ellptl nos otn t no lls ttr wtout wstn too mu rl stt. ˆ ox, rtnl A rtnulr no. 15
16 ˆ trnl ts s urrntly only prtly support u to rstrtons n t Grpvz ntr. Es lotons mt not optml wn trnulr nos r us. ˆ plntxt no no sp t ll, only t no lls r plott. Lts n ll nos sps to llpss rst n tn try out som o t rmnn sps on snl nos. Bus o tr mpt on t ovrll lyout, w v to run lyoutgrp n n orr or ts motons to work. > nornrino(1) <- lst(sp="llps") > nornrino(1) <- lst(sp=(="ox", ="trnl", + ="rl", ="plntxt")) > 1 <- lyoutgrp(1) > rnrgrp(1) A mn ttl... ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~... n suttl To prov vn mor lxlty, t vlus o t sp ttruts n lso usr-n untons. rnrgrp wll ll ts untons ntrnlly, pssn on numr o prmtrs. T most mportnt prmtr s two-y-two mtrx vn t ounn ox o t rsptv no. Ts normton soul us n t sl-n no plottn unton to ontrol t no loton n lso ts sz. No lppn vr ours to ts ounn ox, n t usr s to xtn t no sz yon ts lmts, ovrplottn wt otr nos or s s vry lkly. T tonl prmtrs tt r psss on to 16
17 t unton r: llx, lly, ll, ol, lw, lty, txtcol, styl, ll n ontsz. Consult t lp ps o t lyoutgrp n rnrgrp untons or tls. As n xmpl w wll us unton tt rts rnom trmomtr plots s no lyps n t ollown o unk. Not tt w mk us o t... rumnt to t ll o t pss prmtrs tt w on t rlly n. W lso rmov t lls rom t rp to ty t up lttl. > RnrIno(1) <- lst(ll=null) > myno <- unton(x, ol, ll,...) + symols(x=mn(x[,1]), y=mn(x[,2]), trmomtrs=n(.5, 1, + run(1)), ns=0.5, + =ol, =ll, =TRUE) > nornrino(1) <- lst(sp=lst(=myno, =myno), + ll=(="wt", ="wt"), + ol=(="lk", ="lk")) > 1 <- lyoutgrp(1) > rnrgrp(1) A mn ttl n suttl 5.2 E rrows n rrowtls Smlr to t ontrol o no sps, rnrgrp supports rnt typs o sps or t tps o t s. In unrt rps ts tur s not rlly 17
18 support us s r mrly onntn nos, ty on t onvy ny normton out rton. W n n t mo o our smpl rp to rt to urtr xplor ts tur. > mo(1) <- "rt" T vl vlus or ot rrows n rrowtls o t s r opn, norml, ot, oot, ox, oox, t, mon, omon n non. T lttl lpr unton Nms n us to lst ll vll nms. > RnrIno(1) <- lst(rrow=("~"="ot", "~"="oot", + "~"="mon", "~"="ox", + "~"="ox", "~"="omon"), + rrowtl="t") > 1 <- lyoutgrp(1) > rnrgrp(1) A mn ttl n suttl Tr s lso t opton to pss usr-n unton s rrow or rrowtl prmtr to n vn mor ontrol. Smlr to no sps, t unton s to l to l wt svrl prmtrs: T rst prmtr vs t ntr o t loton o t rrow or tl. T tonl prmtrs ol, lw n lty r olor n ln styls n or t s. > myarrows <- unton(x,...) + { 18
19 + or( n 1:3) + ponts(x,x=,...) + } > RnrIno(1) <- lst(rrowtl=("~"=myarrows)) > 1 <- lyoutgrp(1) > rnrgrp(1) A mn ttl n suttl 6 Sssonno ˆ R vrson ( ), x86_64-p-lnux-nu ˆ Lol: LC_CTYPE=n_US.UTF-8, LC_NUMERIC=C, LC_TIME=n_US.UTF-8, LC_COLLATE=C, LC_MONETARY=n_US.UTF-8, LC_MESSAGES=n_US.UTF-8, LC_PAPER=n_US.UTF-8, LC_NAME=C, LC_ADDRESS=C, LC_TELEPHONE=C, LC_MEASUREMENT=n_US.UTF-8, LC_IDENTIFICATION=C ˆ Runnn unr: Uuntu LTS ˆ Mtrx prouts: ult ˆ BLAS: /om/oul/s-3.6-o/r/l/lrls.so ˆ LAPACK: /om/oul/s-3.6-o/r/l/lrlpk.so 19
20 ˆ Bs pks: s, tsts, rdvs, rps, r, mtos, prlll, stts, utls ˆ Otr pks: BoGnrs , Rrpvz , XML , rp ˆ Lo v nmsp (n not tt): omplr 3.4.2, stts , tools
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