OK thanks That works. :) Ô__ c/ /'_;~~~~kmezhoud (*) \(*) ⴽⴰⵔⵉⵎ ⵎⴻⵣⵀⵓⴷ http://bioinformatics.tn/
On Thu, Nov 13, 2014 at 10:41 PM, William Dunlap <wdun...@tibco.com> wrote: > Use paste(collapse="\n", junk) if you want it as a single string with \n's > in it. > > Bill Dunlap > TIBCO Software > wdunlap tibco.com > > On Thu, Nov 13, 2014 at 1:13 PM, Karim Mezhoud <kmezh...@gmail.com> wrote: > >> Yes Thanks! that works, >> but I loose the \n when I would like to save or edit it. >> >> getTextInWindows is a function that edits any text in editor. >> >> getTextInWindows(summary): without "\n" >> save (file= "junk.txt", junk):without "\n" >> getTextInWindow(capture.output(cat(junk, sep = "\n"))) :No works >> >> Thanks >> >> >> >> >> >> >> >> >> Ô__ >> c/ /'_;~~~~kmezhoud >> (*) \(*) ⴽⴰⵔⵉⵎ ⵎⴻⵣⵀⵓⴷ >> http://bioinformatics.tn/ >> >> >> >> On Thu, Nov 13, 2014 at 9:49 PM, William Dunlap <wdun...@tibco.com> >> wrote: >> >>> Use capture.output(), as in >>> > junk <- capture.output(summary(1:10)) >>> > junk >>> [1] " Min. 1st Qu. Median Mean 3rd Qu. Max. " >>> [2] " 1.00 3.25 5.50 5.50 7.75 10.00 " >>> > cat(junk, sep="\n") >>> Min. 1st Qu. Median Mean 3rd Qu. Max. >>> 1.00 3.25 5.50 5.50 7.75 10.00 >>> >>> >>> >>> Bill Dunlap >>> TIBCO Software >>> wdunlap tibco.com >>> >>> On Thu, Nov 13, 2014 at 12:35 PM, Karim Mezhoud <kmezh...@gmail.com> >>> wrote: >>> >>>> Hi, >>>> >>>> the print of rpart fitting gives the summary of tree >>>> I would like to save the console text of: >>>> fit <- rpart(formula, data) >>>> summary <- print(fit) >>>> >>>> when I look in "summary" I did not find the same thing as in >>>> >>>> >>>> "print(rpart)" >>>> >>>> >>>> [1] "Clinical Data exists" >>>> [1] "merging samples from Clinical and Profile Data" >>>> [1] "Selected formula: DFS_STATUS~." >>>> n= 236 >>>> >>>> node), split, n, loss, yval, (yprob) >>>> * denotes terminal node >>>> >>>> 1) root 236 58 DiseaseFree (0.21610169 0.75423729 0.02966102) >>>> 2) PIK3CA< 302.7615 105 42 DiseaseFree (0.39047619 0.60000000 >>>> 0.00952381) >>>> 4) FGFR1< 941.6309 41 16 (0.60975610 0.36585366 0.02439024) >>>> 8) ANXA1>=2148.882 19 3 (0.84210526 0.10526316 0.05263158) * >>>> 9) ANXA1< 2148.882 22 9 DiseaseFree (0.40909091 0.59090909 >>>> 0.00000000) >>>> 18) RAF1< 2315.279 13 4 (0.69230769 0.30769231 0.00000000) * >>>> 19) RAF1>=2315.279 9 0 DiseaseFree (0.00000000 1.00000000 >>>> 0.00000000) * >>>> 5) FGFR1>=941.6309 64 16 DiseaseFree (0.25000000 0.75000000 >>>> 0.00000000) >>>> 10) CDH2>=153.6887 10 2 (0.80000000 0.20000000 0.00000000) * >>>> 11) CDH2< 153.6887 54 8 DiseaseFree (0.14814815 0.85185185 >>>> 0.00000000) >>>> 22) PCNA< 696.389 7 3 (0.57142857 0.42857143 0.00000000) * >>>> 23) PCNA>=696.389 47 4 DiseaseFree (0.08510638 0.91489362 >>>> 0.00000000) * >>>> 3) PIK3CA>=302.7615 131 16 DiseaseFree (0.07633588 0.87786260 >>>> 0.04580153) * >>>> > >>>> class(summary) >>>> #rpart >>>> >>>> summary >>>> {list(var = c(6, 3, 1, 4, 7, 4, 4, 2, 4, 5, 4, 4, 4), n = c(236, 105, >>>> 41, >>>> 19, 22, 13, 9, 64, 10, 54, 7, 47, 131), wt = c(236, 105, 41, 19, 22, >>>> 13, 9, >>>> 64, 10, 54, 7, 47, 131), dev = c(58, 42, 16, 3, 9, 4, 0, 16, 2, 8, 3, 4, >>>> 16), yval = c(2, 2, 1, 1, 2, 1, 2, 2, 1, 2, 1, 2, 2), complexity = >>>> c(0.0862068965517241, 0.0862068965517241, 0.0775862068965517, 0.01, >>>> 0.0775862068965517, 0.01, 0.01, 0.0862068965517241, 0.01, >>>> 0.0172413793103448, 0.01, 0, 0), ncompete = c(4, 4, 4, 0, 4, 0, 0, 4, >>>> 0, 4, >>>> 0, 0, 0), >>>> nsurrogate = c(5, 5, 5, 0, 5, 0, 0, 5, 0, 5, 0, 0, 0), yval2 = c(2, >>>> 2, >>>> 1, 1, 2, 1, 2, 2, 1, 2, 1, 2, 2, 51, 41, 25, 16, 9, 9, 0, 16, 8, 8, 4, >>>> 4, >>>> 10, 178, 63, 15, 2, 13, 4, 9, 48, 2, 46, 3, 43, 115, 7, 1, 1, 1, 0, 0, >>>> 0, >>>> 0, 0, 0, 0, 0, 6, 0.216101694915254, 0.39047619047619, >>>> 0.609756097560976, >>>> 0.842105263157895, 0.409090909090909, 0.692307692307692, 0, 0.25, 0.8, >>>> 0.148148148148148, 0.571428571428571, 0.0851063829787234, >>>> 0.0763358778625954, 0.754237288135593, 0.6, 0.365853658536585, >>>> 0.105263157894737, >>>> 0.590909090909091, 0.307692307692308, 1, 0.75, 0.2, >>>> 0.851851851851852, >>>> 0.428571428571429, 0.914893617021277, 0.877862595419847, >>>> 0.0296610169491525, 0.00952380952380952, 0.024390243902439, >>>> 0.0526315789473684, 0, 0, 0, 0, 0, 0, 0, 0, 0.0458015267175573, 1, >>>> 0.444915254237288, 0.173728813559322, 0.0805084745762712, >>>> 0.0932203389830508, 0.0550847457627119, 0.038135593220339, >>>> 0.271186440677966, 0.0423728813559322, 0.228813559322034, >>>> 0.0296610169491525, 0.199152542372881, 0.555084745762712))} {c(13, 13, >>>> 13, >>>> 12, 7, 13, 12, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, >>>> 12, >>>> 13, 13, 13, 13, 13, 13, 13, 12, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, >>>> 13, >>>> 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 12, 13, 13, 13, 13, >>>> 13, >>>> 13, 13, 13, 13, 13, 13, 13, 13, 12, 13, 13, 13, 13, 13, 13, 13, 13, 13, >>>> 13, >>>> 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 12, 12, 12, 6, 6, 13, 6, 13, 4, >>>> 13, >>>> 13, 13, 7, 12, 6, 12, 12, 12, 9, 4, 12, 11, 12, 12, 12, 11, 12, 12, 13, >>>> 7, >>>> 4, 12, 12, 4, 9, 7, 13, 12, 7, 12, >>>> 12, 13, 12, 13, 12, 11, 12, 13, 12, 13, 13, 13, 12, 13, 12, 13, 7, 13, >>>> 13, >>>> 12, 13, 13, 13, 13, 13, 12, 13, 13, 13, 13, 13, 13, 13, 13, 13, 12, 13, >>>> 13, >>>> 13, 7, 13, 11, 13, 4, 7, 4, 9, 9, 13, 4, 12, 13, 13, 13, 13, 4, 13, 7, >>>> 4, >>>> 6, 12, 12, 12, 12, 12, 13, 11, 13, 6, 13, 13, 4, 12, 12, 4, 11, 12, 12, >>>> 12, >>>> 13, 13, 13, 12, 9, 9, 9, 4, 9, 4, 4, 4, 11, 13, 4, 4, 9, 12, 6, 4, 9, >>>> 4, 6, >>>> 6, 6, 6, 6, 12)} {rpart(formula = frmla, data = ProfData, method = >>>> "class")} {DFS_STATUS ~ A1CF + ACACA + ACKR2 + AGXT + AHCYL2 + AHSA1 + >>>> AIMP2 + AKR1B1 + AKT1 + AKT1S1 + ANO3 + ANXA1 + APOBR + AQP7 + AR + >>>> ARHGEF26 + ARID1A + ATM + BAK1 + BAX + BCL2 + BCL2L1 + BCL2L11 + BECN1 + >>>> BID + BIRC2 + BRAF + CASP3 + CASP7 + CASP8 + CASP9 + CAT + CAV1 + CCL15 >>>> + >>>> CCNB1 + CCND1 + CCNE1 + CCNE2 + CDH1 + CDH2 + CDHR2 + CDHR5 + CDK1 + >>>> CDKN1A >>>> + CHEK1 + CHEK2 + CHST5 + CLDN7 + CLIC6 + CNTN1 + COL6A2 + COX2 + >>>> CTNNB1 + >>>> DDR2 + DEFA6 + DIABLO + DIRAS1 + DKK3 + DNAJC22 + DVL3 + EDAR + EEF2 + >>>> EEF2K + >>>> EGFR + EIF4E + EIF4EBP1 + ENGASE + ERBB2 + ERBB3 + ERC2 + ERCC1 + >>>> ERRFI1 + ESR1 + FA2H + FAM153A + FAM184A + FGFR1 + FGGY + FN1 + FOXO3 + >>>> GAB2 + GARS + GATA3 + GRID1 + GSK3A + GSK3B + GUCY2C + H3F3AP6 + HOMER2 >>>> + >>>> HPGDS + HSPA1A + HSPA1B + HSPB8 + IFI27 + IGF1R + IGFBP2 + INF2 + >>>> INPP4B + >>>> IRS1 + ITGA2 + JUN + KCNJ5 + KDR + KIAA0226L + KIT + KLK1 + KRAS + LCK + >>>> LPAR1 + LPAR3 + MAP2K1 + MAPK1 + MAPK14 + MAPK4 + MAPK6 + MAPK8 + MAPK9 >>>> + >>>> MAPT + MET + MOGAT3 + MRE11A + MS4A1 + MS4A2 + MSH2 + MSH6 + MTOR + >>>> MYC + MYH7B + NANOS3 + NCOA3 + NDRG1 + NEURL1 + NF2 + NKX2.1 + >>>> NOTCH1 + >>>> NOTCH3 + NPPC + PARK7 + PARP1 + PCDHB11 + PCNA + PDK1 + PDPK1 + PEA15 + >>>> PECAM1 + PGR + PIK3CA + PIK3CB + PIK3CD + PNMAL1 + PRH2 + PRKAA1 + >>>> PRKAA2 + >>>> PRKCA + PRKCD + PSMC4 + PSMD9 + PTCH1 + PTEN + PTK2 + PXN + RAB11A + >>>> RAB25 >>>> + RAD50 + RAD51 + RAF1 + RB1 + REG1B + RORA + RPS6 + SETD2 + SHC1 + >>>> SLC18A1 >>>> + SLC7A8 + SMAD1 + SMAD3 + SMAD4 + SNAI1 + SRC + SSSCA1 + SSUH2 + STAT3 >>>> + >>>> STAT5A + STK11 + STMN4 + SYK + TAZ + TCEAL1 + TGM1 + >>>> TGM2 + TGM3 + TGM4 + TMEM37 + TNFRSF11A + TONSL + TP53 + TP53AIP1 + >>>> TP53BP1 + TRIL + TSC2 + TSPO2 + VASP + WWTR1 + XBP1 + XBP1P1 + XIAP + >>>> XRCC1 >>>> + XRCC5 + YBX1 + YWHAE + YY1AP1} {c(0.0862068965517241, >>>> 0.0775862068965517, >>>> 0.0172413793103448, 0.01, 0, 3, 5, 6, 1, 0.724137931034483, >>>> 0.568965517241379, 0.551724137931034, 1, 1.22413793103448, >>>> 1.3448275862069, >>>> 1.41379310344828, 0.114035482086724, 0.121475068159872, >>>> 0.124592485529312, >>>> 0.12611980528159)} class {list(prior = c(0.216101694915254, >>>> 0.754237288135593, 0.0296610169491525), loss = c(0, 1, 1, 1, 0, 1, 1, 1, >>>> 0), split = 1)} {list(minsplit = 20, minbucket = 7, cp = 0.01, >>>> maxcompete = >>>> 4, maxsurrogate = 5, usesurrogate = 2, surrogatestyle = 0, maxdepth = >>>> 30, >>>> xval = 10)} {list(summary = function (yval, dev, wt, ylevel, digits) >>>> { >>>> nclass <- (ncol(yval) - 2)/2 >>>> group <- yval[, 1] >>>> counts <- yval[, 1 + (1:nclass)] >>>> yprob <- yval[, 1 + nclass + 1:nclass] >>>> nodeprob <- yval[, 2 * nclass + 2] >>>> if (!is.null(ylevel)) >>>> group <- ylevel[group] >>>> temp1 <- formatg(counts, format = "%5g") >>>> temp2 <- formatg(yprob, format = "%5.3f") >>>> if (nclass > 1) { >>>> temp1 <- apply(matrix(temp1, ncol = nclass), 1, paste, collapse >>>> = " >>>> ") >>>> temp2 <- apply(matrix(temp2, ncol = nclass), 1, paste, collapse >>>> = " >>>> ") >>>> } >>>> dev <- dev/(wt[1] * nodeprob) >>>> paste0(" predicted class=", format(group, justify = "left"), " >>>> expected loss=", formatg(dev, digits), " P(node) =", formatg(nodeprob, >>>> digits), "\n", " class counts: ", temp1, "\n", " probabilities: ", >>>> temp2) >>>> }, print = function (yval, ylevel, digits) >>>> { >>>> temp <- if (is.null(ylevel)) >>>> as.character(yval[, 1]) >>>> else ylevel[yval[, 1]] >>>> nclass <- (ncol(yval) - 2)/2 >>>> yprob <- if (nclass < 5) >>>> format(yval[, 1 + nclass + 1:nclass], digits = digits, nsmall = >>>> digits) >>>> else formatg(yval[, 1 + nclass + 1:nclass], digits = 2) >>>> if (!is.matrix(yprob)) >>>> yprob <- matrix(yprob, nrow = 1) >>>> temp <- paste0(temp, " (", yprob[, 1]) >>>> for (i in 2:ncol(yprob)) temp <- paste(temp, yprob[, i], sep = " ") >>>> temp <- paste0(temp, ")") >>>> temp >>>> }, text = function (yval, dev, wt, ylevel, digits, n, use.n) >>>> { >>>> nclass <- (ncol(yval) - 2)/2 >>>> group <- yval[, 1] >>>> counts <- yval[, 1 + (1:nclass)] >>>> if (!is.null(ylevel)) >>>> group <- ylevel[group] >>>> temp1 <- formatg(counts, digits) >>>> if (nclass > 1) >>>> temp1 <- apply(matrix(temp1, ncol = nclass), 1, paste, collapse >>>> = >>>> "/") >>>> >>>> ....................... >>>> >>>> How can I save print(fit)? >>>> Thank? >>>> >>>> Ô__ >>>> c/ /'_;~~~~kmezhoud >>>> (*) \(*) ⴽⴰⵔⵉⵎ ⵎⴻⵣⵀⵓⴷ >>>> http://bioinformatics.tn/ >>>> >>>> [[alternative HTML version deleted]] >>>> >>>> ______________________________________________ >>>> 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. >>>> >>> >>> >> > [[alternative HTML version deleted]] ______________________________________________ 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.
