X-Git-Url: http://iramuteq.org/git?p=iramuteq;a=blobdiff_plain;f=PrintRScript.py;h=d925a4d84094e14fc9bb05126a755a8601239ec9;hp=a2dde7f622058d11de86fdef186cbfc0c70374e2;hb=3dffb481f7f3a6b8411ac6bb0edfc3536be58377;hpb=a57eea4fed2471fdf373ea4ce5860244530eec24 diff --git a/PrintRScript.py b/PrintRScript.py index a2dde7f..d925a4d 100644 --- a/PrintRScript.py +++ b/PrintRScript.py @@ -164,15 +164,17 @@ def RchdTxt(DicoPath, RscriptPath, mincl, classif_mode, nbt = 9, svdmethod = 'sv """ % ffr(DicoPath['TableUc2']) txt += """ log1 <- "%s" - chd1<-CHD(data1, x = nbt, mode.patate = mode.patate, svd.method = - svd.method, libsvdc.path = libsvdc.path, log.file = log1) + #print('FIXME : source newCHD') + #source('/home/pierre/workspace/iramuteq/Rscripts/newCHD.R') + #chd1<-CHD(data1, x = nbt, mode.patate = mode.patate, svd.method = svd.method, libsvdc.path = libsvdc.path, find='matrix', sample=20, amp=500) + chd1<-CHD(data1, x = nbt, mode.patate = mode.patate, svd.method = svd.method, libsvdc.path = libsvdc.path)#, log.file = log1) """ % ffr(DicoPath['log-chd1.txt']) if classif_mode == 0: txt += """ log2 <- "%s" chd2<-CHD(data2, x = nbt, mode.patate = mode.patate, svd.method = - svd.method, libsvdc.path = libsvdc.path) log.file = log2) + svd.method, libsvdc.path = libsvdc.path)#, log.file = log2) """ % ffr(DicoPath['log-chd2.txt']) txt += """ @@ -196,21 +198,29 @@ def RchdTxt(DicoPath, RscriptPath, mincl, classif_mode, nbt = 9, svdmethod = 'sv txt += """ classif_mode <- %i mincl <- %i + if (mincl == 0) {mincl <- round(nrow(chd1$n1)/(nbt+1))} uceout <- "%s" + write.csv2(chd1$n1, file="%s") if (classif_mode == 0) { chd.result <- Rchdtxt(uceout, chd1, chd2 = chd2, mincl = mincl,classif_mode = classif_mode, nbt = nbt) + classeuce1 <- chd.result$cuce1 + tree.tot1 <- make_tree_tot(chd1) + tree.cut1 <- make_dendro_cut_tuple(tree.tot1$dendro_tuple, chd.result$coord_ok, classeuce1, 1, nbt) + } else { - chd.result <- Rchdtxt(uceout, chd1, chd2 = chd1, mincl = mincl,classif_mode = classif_mode, nbt = nbt) + #chd.result <- Rchdtxt(uceout, chd1, chd2 = chd1, mincl = mincl,classif_mode = classif_mode, nbt = nbt) + tree.tot1 <- make_tree_tot(chd1) + terminales <- find.terminales(chd1$n1, chd1$list_mere, chd1$list_fille, mincl) + tree.cut1 <- make.classes(terminales, chd1$n1, tree.tot1$tree.cl, chd1$list_fille) + write.csv2(tree.cut1$n1, uceout) + chd.result <- tree.cut1 } - n1 <- chd.result$n1 - classeuce1 <- chd.result$cuce1 - classes<-n1[,ncol(n1)] - write.csv2(n1, file="%s") - rm(n1) - """ % (classif_mode, mincl, ffr(DicoPath['uce']), ffr(DicoPath['n1.csv'])) + classes<-chd.result$n1[,ncol(chd.result$n1)] + write.csv2(chd.result$n1, file="%s") + """ % (classif_mode, mincl, ffr(DicoPath['uce']), ffr(DicoPath['n1-1.csv']), ffr(DicoPath['n1.csv'])) txt += """ - tree.tot1 <- make_tree_tot(chd1) +# tree.tot1 <- make_tree_tot(chd1) # open_file_graph("%s", widt = 600, height=400) # plot(tree.tot1$tree.cl) # dev.off() @@ -226,8 +236,7 @@ def RchdTxt(DicoPath, RscriptPath, mincl, classif_mode, nbt = 9, svdmethod = 'sv """ % ffr(DicoPath['arbre2'] ) txt += """ - tree.cut1 <- make_dendro_cut_tuple(tree.tot1$dendro_tuple, chd.result$coord_ok, classeuce1, 1, nbt) - save(tree.cut1, file="%s") + save(tree.cut1, file="%s") open_file_graph("%s", width = 600, height=400) plot.dendropr(tree.cut1$tree.cl,classes, histo=TRUE) @@ -337,9 +346,14 @@ datasup<-read.csv2("%s", header = FALSE, sep = ';',quote = '\"', row.names = 1, dataet<-read.csv2("%s", header = FALSE, sep = ';',quote = '\"', row.names = 1, na.strings = 'NA') """ % (ffr(DictChdTxtOut['Contout']), ffr(DictChdTxtOut['ContSupOut']), ffr(DictChdTxtOut['ContEtOut'])) txt += """ -tablesqrpact<-BuildProf(as.matrix(dataact),n1,clnb) -tablesqrpsup<-BuildProf(as.matrix(datasup),n1,clnb) -tablesqrpet<-BuildProf(as.matrix(dataet),n1,clnb) +print('ATTENTION NEW BUILD PROF') +#tablesqrpact<-BuildProf(as.matrix(dataact),n1,clnb) +#tablesqrpsup<-BuildProf(as.matrix(datasup),n1,clnb) +#tablesqrpet<-BuildProf(as.matrix(dataet),n1,clnb) +tablesqrpact<-new.build.prof(as.matrix(dataact),n1,clnb) +tablesqrpsup<-new.build.prof(as.matrix(datasup),n1,clnb) +tablesqrpet<-new.build.prof(as.matrix(dataet),n1,clnb) + """ txt += """ PrintProfile(n1,tablesqrpact[4],tablesqrpet[4],tablesqrpact[5],tablesqrpet[5],clnb,"%s","%s",tablesqrpsup[4],tablesqrpsup[5]) @@ -723,6 +737,7 @@ class PrintSimiScript(PrintRScript) : else : txt += """ word <- FALSE + index <- NULL """ txt += """ dm <-readMM(dm.path) @@ -847,10 +862,13 @@ class PrintSimiScript(PrintRScript) : txt += """ mat <- graph.word(mat, index) cs <- colSums(mat) - if (length(cs)) mat <- mat[,-which(cs==0)] + if (length(which(cs==0))) mat <- mat[,-which(cs==0)] rs <- rowSums(mat) - if (length(rs)) mat <- mat[-which(rs==0),] - if (length(cs)) dm <- dm[, -which(cs==0)] + if (length(which(rs==0))) mat <- mat[-which(rs==0),] + if (length(which(cs==0))) dm <- dm[,-which(cs==0)] + if (word) { + index <- which(colnames(mat)==forme) + } """ if self.parametres['layout'] == 0 : layout = 'random' @@ -858,6 +876,8 @@ class PrintSimiScript(PrintRScript) : if self.parametres['layout'] == 2 : layout = 'frutch' if self.parametres['layout'] == 3 : layout = 'kawa' if self.parametres['layout'] == 4 : layout = 'graphopt' + if self.parametres['layout'] == 5 : layout = 'spirale' + if self.parametres['layout'] == 6 : layout = 'spirale3D' self.filename='' @@ -877,7 +897,7 @@ class PrintSimiScript(PrintRScript) : while os.path.exists(os.path.join(dirout,'web_'+str(graphnb))): graphnb +=1 self.filename = ffr(os.path.join(dirout,'web_'+str(graphnb))) - os.mkdir(self.filename) + os.mkdir(self.filename) self.filename = os.path.join(self.filename, 'gexf.gexf') if self.parametres['type_graph'] == 4 : graphnb = 1 @@ -1064,7 +1084,7 @@ class PrintSimiScript(PrintRScript) : txt += """ eff <- colSums(dm) x <- list(mat = mat, eff = eff) - graph.simi <- do.simi(x, method='%s', seuil = seuil, p.type = '%s', layout.type = '%s', max.tree = %s, coeff.vertex=%s, coeff.edge = %s, minmaxeff = minmaxeff, vcexminmax = vcexminmax, cex = cex, coords = coords, communities = communities, halo = halo) + graph.simi <- do.simi(x, method='%s', seuil = seuil, p.type = '%s', layout.type = '%s', max.tree = %s, coeff.vertex=%s, coeff.edge = %s, minmaxeff = minmaxeff, vcexminmax = vcexminmax, cex = cex, coords = coords, communities = communities, halo = halo, index.word=index) """ % (method, type, layout, arbremax, coeff_tv, coeff_te) if self.parametres.get('bystar',False) : @@ -1316,7 +1336,7 @@ class LabbeScript(PrintRScript) : self.analyse.parent.RscriptsPath['Rgraph']]) txt = """ tab <- read.csv2("%s", header=TRUE, sep=';', row.names=1) - """ % (self.pathout['tableafcm.csv']) + """ % (ffr(self.pathout['tableafcm.csv'])) txt += """ dist.mat <- dist.labbe(tab) dist.mat <- as.dist(dist.mat, upper=F, diag=F) @@ -1328,7 +1348,26 @@ class LabbeScript(PrintRScript) : par(cex=1.2) plot.phylo(as.phylo(chd), type='unrooted', lab4ut="axial") dev.off() - """ % (self.pathout['distmat.csv'], self.pathout['dist-labbe.png']) + """ % (ffr(self.pathout['distmat.csv']), ffr(self.pathout['labbe-tree.png'])) + txt +=""" + open_file_graph("%s", width=1000, height=1000, svg=F) + par(mar=c(10,1,1,10)) + heatmap(as.matrix(dist.mat), symm = T, distfun=function(x) as.dist(x), margins=c(10,10)) + dev.off() + """ % ffr(self.pathout['labbe-heatmap.png']) + txt += """ + #http://stackoverflow.com/questions/3081066/what-techniques-exists-in-r-to-visualize-a-distance-matrix + dst <- data.matrix(dist.mat) + dim <- ncol(dst) + rn <- row.names(as.matrix(dist.mat)) + open_file_graph("%s", width=1500, height=1000, svg=F) + par(mar=c(10,10,3,3)) + image(1:dim, 1:dim, dst, axes = FALSE, xlab="", ylab="") + axis(1, 1:dim, rn, cex.axis = 0.9, las=3) + axis(2, 1:dim, rn, cex.axis = 0.9, las=1) + text(expand.grid(1:dim, 1:dim), sprintf("%%0.2f", dst), cex=0.6) + dev.off() + """ % ffr(self.pathout['labbe-matrix.png']) self.add(txt) self.write() @@ -1341,7 +1380,7 @@ class ChronoChi2Script(PrintRScript) : dendrof <- "%s" load(inRData) load(dendrof) - """ % (self.pathout['RData.RData'], self.pathout['dendrogramme.RData']) + """ % (ffr(self.pathout['RData.RData']), ffr(self.pathout['dendrogramme.RData'])) txt += """ svg <- %s """ % self.parametres['svg'] @@ -1355,7 +1394,7 @@ class ChronoChi2Script(PrintRScript) : ptc <- tcp/sum(tcp) dpt <- t(dpt) dd <- dpt - """ % self.parametres['var'] + """ % self.parametres['var'].replace(u'*', u"\\\\*") txt += """ classes <- n1[,ncol(n1)] tcl <- table(classes) @@ -1396,8 +1435,10 @@ class ChronoChi2Script(PrintRScript) : layout(mat.graphic, heights=heights.graphic, widths=c(0.15,0.85)) par(mar=c(0,0,0,0)) tree.toplot <- tree.cut1$tree.cl - tree.toplot$tip.label <- paste('classe ', tree.toplot$tip.label) - plot.phylo(tree.toplot,label.offset=0.1, cex=1.1, no.margin=T) + num.label <- as.numeric(tree.cut1$tree.cl$tip.label) + col.tree <- rainbow(length(num.label))[num.label] + #tree.toplot$tip.label <- paste('classe ', tree.toplot$tip.label) + plot.phylo(tree.toplot,label.offset=0.1, cex=1.1, no.margin=T, tip.color = col.tree) for (i in clod) { print(i) par(mar=c(0,0,0,0)) @@ -1434,7 +1475,7 @@ class ChronoPropScript(PrintRScript) : dendrof <- "%s" load(inRData) load(dendrof) - """ % (self.pathout['RData.RData'], self.pathout['dendrogramme.RData']) + """ % (ffr(self.pathout['RData.RData']), ffr(self.pathout['dendrogramme.RData'])) txt += """ svg <- %s """ % self.parametres['svg'] @@ -1448,7 +1489,7 @@ class ChronoPropScript(PrintRScript) : ptc <- tcp/sum(tcp) dpt <- t(dpt) dd <- dpt - """ % self.parametres['var'] + """ % self.parametres['var'].replace(u'*', u"\\\\*") txt += """ classes <- n1[,ncol(n1)] tcl <- table(classes) @@ -1470,4 +1511,8 @@ class ChronoPropScript(PrintRScript) : self.add(txt) self.write() +class ReDoProfScript(PrintRScript) : + def make_script(self) : + self.sources([self.analyse.parent.RscriptsPath['chdfunct.R']]) + print self.parametres