X-Git-Url: http://iramuteq.org/git?p=iramuteq;a=blobdiff_plain;f=PrintRScript.py;h=4987b21ebea0ba85b3c80a13dd3b7eadba61dbe0;hp=8d85e7100e267c5eb9b0e5898befd1c6ba7ad653;hb=ef45aa7e5e55a37956ce86dc4ce86471f11b018d;hpb=ea75400310e91c45b6a705119b2e33afc0933e3e diff --git a/PrintRScript.py b/PrintRScript.py index 8d85e71..4987b21 100644 --- a/PrintRScript.py +++ b/PrintRScript.py @@ -109,7 +109,7 @@ class Alceste2(PrintRScript) : # -def RchdTxt(DicoPath, RscriptPath, mincl, classif_mode, nbt = 9, libsvdc = False, libsvdc_path = None, R_max_mem = False): +def RchdTxt(DicoPath, RscriptPath, mincl, classif_mode, nbt = 9, svdmethod = 'svdR', libsvdc = False, libsvdc_path = None, R_max_mem = False, mode_patate = False): txt = """ source("%s") source("%s") @@ -124,17 +124,30 @@ def RchdTxt(DicoPath, RscriptPath, mincl, classif_mode, nbt = 9, libsvdc = False txt += """ nbt <- %i """ % nbt - if libsvdc : + if svdmethod == 'svdlibc' and libsvdc : txt += """ - libsvdc <- TRUE + svd.method <- 'svdlibc' libsvdc.path <- "%s" """ % ffr(libsvdc_path) + elif svdmethod == 'irlba' : + txt += """ + library(irlba) + svd.method <- 'irlba' + libsvdc.path <- NULL + """ else : txt += """ - libsvdc <- FALSE + svd.method = 'svdR' libsvdc.path <- NULL """ - + if mode_patate : + txt += """ + mode.patate = TRUE + """ + else : + txt += """ + mode.patate = FALSE + """ txt +=""" library(Matrix) data1 <- readMM("%s") @@ -148,14 +161,13 @@ def RchdTxt(DicoPath, RscriptPath, mincl, classif_mode, nbt = 9, libsvdc = False data2 <- as(data2, "dgCMatrix") row.names(data2) <- 1:nrow(data2) """ % DicoPath['TableUc2'] - #log.info('ATTENTION ############# MODEPATATE ####################') txt += """ - chd1<-CHD(data1, x = nbt, mode.patate = FALSE, libsvdc = libsvdc, libsvdc.path = libsvdc.path) + chd1<-CHD(data1, x = nbt, mode.patate = mode.patate, svd.method = svd.method, libsvdc.path = libsvdc.path) """ if classif_mode == 0: txt += """ - chd2<-CHD(data2, x = nbt, libsvdc = libsvdc, libsvdc.path = libsvdc.path) + chd2<-CHD(data2, x = nbt, mode.patate = mode.patate, svd.method = svd.method, libsvdc.path = libsvdc.path) """ else: txt += """ @@ -173,12 +185,12 @@ def RchdTxt(DicoPath, RscriptPath, mincl, classif_mode, nbt = 9, libsvdc = False """ % DicoPath['listeuce2'] txt += """ -# rm(data1) + rm(data1) """ if classif_mode == 0: txt += """ -# rm(data2) + rm(data2) """ txt += """ chd.result <- Rchdtxt("%s",mincl=%i,classif_mode=%i, nbt = nbt) @@ -275,7 +287,7 @@ def RchdQuest(DicoPath, RscriptPath, nbcl = 10, mincl = 10): chd.result<-Rchdquest("%s","%s","%s", nbt = nbt, mincl = mincl) n1 <- chd.result$n1 classeuce1 <- chd.result$cuce1 - """ % (DicoPath['Act01'], DicoPath['listeuce1'], DicoPath['uce']) + """ % (DicoPath['mat01'], DicoPath['listeuce1'], DicoPath['uce']) txt += """ tree_tot1 <- make_tree_tot(chd.result$chd) @@ -374,10 +386,14 @@ write.csv2(gbcluster,file="%s") txt += """ PARCEX<-%s - xmin <- min(afc$rowcoord[,1]) + (0.1 * min(afc$rowcoord[,1])) - xmax <- max(afc$rowcoord[,1]) + (0.1 * max(afc$rowcoord[,1])) - ymin <- min(afc$rowcoord[,2]) + (0.1 * min(afc$rowcoord[,2])) - ymax <- max(afc$rowcoord[,2]) + (0.1 * max(afc$rowcoord[,2])) + xmin <- min(afc$rowcoord[,1], na.rm = TRUE) + (0.1 * min(afc$rowcoord[,1], na.rm = TRUE)) + xmax <- max(afc$rowcoord[,1], na.rm = TRUE) + (0.1 * max(afc$rowcoord[,1], na.rm = TRUE)) + ymin <- min(afc$rowcoord[,2], na.rm = TRUE) + (0.1 * min(afc$rowcoord[,2], na.rm = TRUE)) + ymax <- max(afc$rowcoord[,2], na.rm = TRUE) + (0.1 * max(afc$rowcoord[,2], na.rm = TRUE)) + print(xmin) + print(xmax) + print(ymin) + print(ymax) """ % taillecar txt += """ PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", what='coord', deb=1, fin=(debsup-1), xlab = xlab, ylab = ylab, xmin=xmin, xmax=xmax, ymin = ymin, ymax=ymax) @@ -431,6 +447,9 @@ def write_afc_graph(self): if self.param['tchi'] : tchi = 'TRUE' else : tchi = 'FALSE' + if self.param['svg'] : svg = 'TRUE' + else : svg = 'FALSE' + with open(self.RscriptsPath['afc_graph'], 'r') as f: txt = f.read() @@ -460,7 +479,8 @@ def write_afc_graph(self): tchi,\ self.param['tchi_min'],\ self.param['tchi_max'],\ - ffr(os.path.dirname(self.fileout))) + ffr(os.path.dirname(self.fileout)),\ + svg) return scripts def print_simi3d(self): @@ -535,9 +555,29 @@ def barplot(table, rownames, colnames, rgraph, tmpgraph, intxt = False) : if not intxt : #FIXME txt = """ - inf <- NA di <- matrix(data=%s, nrow=%i, byrow = TRUE) - di[is.na(di)] <- max(di, na.rm=TRUE) + 2 + toinf <- which(di == Inf) + tominf <- which(di == -Inf) + if (length(toinf)) { + di[toinf] <- NA + valmax <- max(di, na.rm = TRUE) + if (valmax <= 0) { + valmax <- 2 + } else { + valmax <- valmax + 2 + } + di[toinf] <- valmax + } + if (length(tominf)) { + di[tominf] <- NA + valmin <- min(di, na.rm = TRUE) + if (valmin >=0) { + valmin <- -2 + } else { + valmin <- valmin - 2 + } + di[tominf] <- valmin + } rownames(di)<- %s colnames(di) <- %s """ % (txttable, rownb, rownames, colnames) @@ -553,7 +593,20 @@ def barplot(table, rownames, colnames, rgraph, tmpgraph, intxt = False) : par(mar=c(0,0,0,0)) layout(matrix(c(1,2),1,2, byrow=TRUE),widths=c(3,lcm(7))) par(mar=c(2,2,1,0)) - coord <- barplot(as.matrix(di), beside = TRUE, col = color, space = c(0.1,0.6)) + yp = ifelse(length(toinf), 0.2, 0) + ym = ifelse(length(tominf), 0.2, 0) + ymin <- ifelse(!length(which(di < 0)), 0, min(di) - ym) + coord <- barplot(as.matrix(di), beside = TRUE, col = color, space = c(0.1,0.6), ylim=c(ymin, max(di) + yp)) + if (length(toinf)) { + coordinf <- coord[toinf] + valinf <- di[toinf] + text(x=coordinf, y=valinf + 0.1, 'i') + } + if (length(tominf)) { + coordinf <- coord[toinf] + valinf <- di[toinf] + text(x=coordinf, y=valinf - 0.1, 'i') + } c <- colMeans(coord) c1 <- c[-1] c2 <- c[-length(c)] @@ -644,29 +697,37 @@ class PrintSimiScript(PrintRScript) : self.txtgraph = '' self.packages(['igraph', 'proxy', 'Matrix']) self.sources([self.analyse.parent.RscriptsPath['simi'], self.analyse.parent.RscriptsPath['Rgraph']]) - txt = """ - dm.path <- "%s" - cn.path <- "%s" - selected.col <- "%s" - """ % (self.pathout['mat01.csv'], self.pathout['actives.csv'], self.pathout['selected.csv']) - txt += """ - dm <-readMM(dm.path) - cn <- read.table(cn.path, sep=';', quote='"') - colnames(dm) <- cn[,1] - sel.col <- read.csv2(selected.col) - dm <- dm[, sel.col[,1] + 1] - """ - - if self.parametres['coeff'] == 0 : - method = 'cooc' + txt = '' + if not self.parametres['keep_coord'] : + txt += """ + dm.path <- "%s" + cn.path <- "%s" + selected.col <- "%s" + """ % (self.pathout['mat01.csv'], self.pathout['actives.csv'], self.pathout['selected.csv']) txt += """ - method <- 'cooc' - mat <- make.a(dm) + dm <-readMM(dm.path) + cn <- read.table(cn.path, sep='\t', quote='"') + colnames(dm) <- cn[,1] + sel.col <- read.csv2(selected.col) + dm <- dm[, sel.col[,1] + 1] """ else : txt += """ - dm <- as.matrix(dm) - """ + load("%s") + """ % self.pathout['RData.RData'] + + if self.parametres['coeff'] == 0 : + method = 'cooc' + if not self.parametres['keep_coord'] : + txt += """ + method <- 'cooc' + mat <- make.a(dm) + """ + else : + if not self.parametres['keep_coord'] : + txt += """ + dm <- as.matrix(dm) + """ if self.parametres['coeff'] == 1 : method = 'prcooc' txt += """ @@ -675,27 +736,31 @@ class PrintSimiScript(PrintRScript) : """ elif self.analyse.indices[self.parametres['coeff']] == 'binomial' : method = 'binomial' - txt += """ - method <- 'binomial' - mat <- binom.sim(dm) - """ + if not self.parametres['keep_coord'] : + txt += """ + method <- 'binomial' + mat <- binom.sim(dm) + """ elif self.parametres['coeff'] != 0 : method = self.analyse.indices[self.parametres['coeff']] + if not self.parametres['keep_coord'] : + txt += """ + method <-"%s" + mat <- simil(dm, method = method, diag = TRUE, upper = TRUE, by_rows = FALSE) + """ % self.analyse.indices[self.parametres['coeff']] + if not self.parametres['keep_coord'] : txt += """ - method <-"%s" - mat <- simil(dm, method = method, diag = TRUE, upper = TRUE, by_rows = FALSE) - """ % self.analyse.indices[self.parametres['coeff']] - txt += """ - mat <- as.matrix(stats::as.dist(mat,diag=TRUE,upper=TRUE)) - mat[is.na(mat)] <- 0 - mat[is.infinite(mat)] <- 0 - """ + mat <- as.matrix(stats::as.dist(mat,diag=TRUE,upper=TRUE)) + mat[is.na(mat)] <- 0 + mat[is.infinite(mat)] <- 0 + """ if self.parametres['layout'] == 0 : layout = 'random' if self.parametres['layout'] == 1 : layout = 'circle' if self.parametres['layout'] == 2 : layout = 'frutch' if self.parametres['layout'] == 3 : layout = 'kawa' if self.parametres['layout'] == 4 : layout = 'graphopt' + self.filename='' if self.parametres['type_graph'] == 0 : type = 'tkplot' if self.parametres['type_graph'] == 1 : @@ -793,14 +858,13 @@ class PrintSimiScript(PrintRScript) : txt += """ et <- list() """ - print self.parametres - for i,et in enumerate(self.parametres['stars']) : + for i, line in enumerate(self.parametres['listet']) : txt+= """ et[[%i]] <- c(%s) - """ % (i+1, ','.join(et[1:])) + """ % (i+1, ','.join([`val + 1` for val in line])) txt+= """ unetoile <- c('%s') - """ % ("','".join([val[0] for val in self.tableau.etline])) + """ % ("','".join([val for val in self.parametres['selectedstars']])) txt += """ fsum <- NULL rs <- rowSums(dm) @@ -825,7 +889,7 @@ class PrintSimiScript(PrintRScript) : cols <- vertex.label.color chivertex.size <- norm.vec(toblack, vcexminmax[1], vcexminmax[2]) - """ % (self.parent.RscriptsPath['chdfunct']) + """ % (self.analyse.parent.RscriptsPath['chdfunct']) else : txt += """ vertex.label.color <- 'black'