From 45e272d7c7cb8fcfc079403631d8a4dcacc795ce Mon Sep 17 00:00:00 2001 From: Pierre Ratinaud Date: Sun, 31 Dec 2017 12:30:32 +0100 Subject: [PATCH] ... --- PrintRScript.py | 152 +++++++++++++++++++++++++++++++++++++++++++++++++++----- 1 file changed, 139 insertions(+), 13 deletions(-) diff --git a/PrintRScript.py b/PrintRScript.py index d925a4d..dd053e3 100644 --- a/PrintRScript.py +++ b/PrintRScript.py @@ -13,11 +13,14 @@ import logging log = logging.getLogger('iramuteq.printRscript') class PrintRScript : - def __init__ (self, analyse): + def __init__ (self, analyse, parametres = None): log.info('Rscript') self.pathout = analyse.pathout self.analyse = analyse - self.parametres = analyse.parametres + if parametres is None : + self.parametres = analyse.parametres + else : + self.parametres = parametres #self.scriptout = ffr(self.pathout['lastRscript.R']) self.scriptout = self.pathout['temp'] self.script = u"#Script genere par IRaMuTeQ - %s\n" % datetime.now().ctime() @@ -164,10 +167,10 @@ def RchdTxt(DicoPath, RscriptPath, mincl, classif_mode, nbt = 9, svdmethod = 'sv """ % ffr(DicoPath['TableUc2']) txt += """ log1 <- "%s" - #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) + 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', select.next='size', 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: @@ -464,12 +467,20 @@ def write_afc_graph(self): if self.param['svg'] : svg = 'TRUE' else : svg = 'FALSE' + if self.param['typegraph'] == 4 : + nodesfile = os.path.join(os.path.dirname(self.fileout),'nodes.csv') + edgesfile = os.path.join(os.path.dirname(self.fileout),'edges.csv') + else : + nodesfile = 'NULL' + edgesfile = 'NULL' + with open(self.RscriptsPath['afc_graph'], 'r') as f: txt = f.read() # self.DictPathOut['RData'], \ scripts = txt % (ffr(self.RscriptsPath['Rgraph']),\ self.param['typegraph'], \ + edgesfile, nodesfile, \ self.param['what'], \ self.param['facteur'][0],\ self.param['facteur'][1], \ @@ -606,7 +617,7 @@ def barplot(table, parametres, intxt = False) : height <- %i open_file_graph("%s",width = width, height = height, svg = %s) par(mar=c(0,0,0,0)) - layout(matrix(c(1,2),1,2, byrow=TRUE),widths=c(3,lcm(7))) + layout(matrix(c(1,2),1,2, byrow=TRUE),widths=c(3,lcm(12))) par(mar=c(8,4,1,0)) yp = ifelse(length(toinf), 0.2, 0) ym = ifelse(length(tominf), 0.2, 0) @@ -741,7 +752,7 @@ class PrintSimiScript(PrintRScript) : """ txt += """ dm <-readMM(dm.path) - cn <- read.table(cn.path, sep='\t', quote='"') + cn <- read.table(cn.path, sep="\t", quote='"') colnames(dm) <- cn[,1] if (file.exists(selected.col)) { sel.col <- read.csv2(selected.col, header = FALSE) @@ -798,7 +809,7 @@ class PrintSimiScript(PrintRScript) : txt += """ load("%s") """ % ffr(self.pathout['RData.RData']) - + if self.parametres['coeff'] == 0 : method = 'cooc' if not self.parametres['keep_coord'] : @@ -806,6 +817,13 @@ class PrintSimiScript(PrintRScript) : method <- 'cooc' mat <- make.a(dm) """ + elif self.analyse.indices[self.parametres['coeff']] == 'Jaccard' : + method = 'Jaccard' + if not self.parametres['keep_coord'] : + txt += """ + method <- 'Jaccard' + mat <- sparse.jaccard(dm) + """ else : if not self.parametres['keep_coord'] : txt += """ @@ -824,7 +842,7 @@ class PrintSimiScript(PrintRScript) : method <- 'binomial' mat <- binom.sim(dm) """ - elif self.parametres['coeff'] != 0 : + elif self.parametres['coeff'] != 0 and self.analyse.indices[self.parametres['coeff']] != 'Jaccard': method = self.analyse.indices[self.parametres['coeff']] if not self.parametres['keep_coord'] : txt += """ @@ -1147,6 +1165,17 @@ class PrintSimiScript(PrintRScript) : """ % svg txt += """ vertex.col <- cols + col.from.proto <- F + if (col.from.proto) { + proto.col <- read.table('/tmp/matcol.csv') + v.proto.names <- make.names(proto.col[,1]) + v.proto.col <- as.character(proto.col[,2]) + v.proto.col[which(v.proto.col=='black')] <- 'yellow' + v.names <- V(graph.simi$graph)$name + num.color <- sapply(v.names, function(x) {if (x %%in%% v.proto.names) {v.proto.col[which(v.proto.names==x)]} else {'pink'}}) + vertex.col <- num.color + V(graph.simi$graph)$proto.color <- vertex.col + } if (!is.null(graph.simi$com)) { com <- graph.simi$com colm <- rainbow(length(com)) @@ -1212,7 +1241,7 @@ class ProtoScript(PrintRScript) : } mat <- read.csv2("%s", header = FALSE, row.names=1, sep='\t', quote='"', dec='.') open_file_graph("%s",height=800, width=1000) - prototypical(mat, mfreq = %s, mrank = %s, cloud = FALSE, cexrange=c(1,2.4), cexalpha= c(0.4, 1), type = '%s') + prototypical(mat, mfreq = %s, mrank = %s, cloud = FALSE, cexrange=c(1,2.4), cexalpha= c(0.4, 1), type = '%s', mat.col.path='/tmp/matcol.csv') dev.off() """ % (ffr(self.analyse.pathout['table.csv']), ffr(self.analyse.pathout['proto.png']), self.parametres['limfreq'], self.parametres['limrang'], self.parametres['typegraph']) self.add(txt) @@ -1256,7 +1285,12 @@ class MergeGraphes(PrintRScript) : self.add(txt) self.sources([self.analyse.parent.RscriptsPath['simi']]) txt = """ - ng <- merge.graph(graphs) + merge.type <- 'proto' + if (merge.type == 'normal') { + ng <- merge.graph(graphs) + } else { + ng <- merge.graph.proto(graphs) + } ngraph <- list(graph=ng, layout=layout.fruchterman.reingold(ng, dim=3), labex.cex=V(ng)$weight) write.graph(ng, "%s", format = 'graphml') """ % ffr(self.parametres['grapheout']) @@ -1362,12 +1396,27 @@ class LabbeScript(PrintRScript) : rn <- row.names(as.matrix(dist.mat)) open_file_graph("%s", width=1500, height=1000, svg=F) par(mar=c(10,10,3,3)) - image(1:dim, 1:dim, dst, axes = FALSE, xlab="", ylab="") + image(1:dim, 1:dim, dst, axes = FALSE, xlab="", ylab="", col=heat.colors(99), breaks=seq(0.01,1,0.01)) axis(1, 1:dim, rn, cex.axis = 0.9, las=3) axis(2, 1:dim, rn, cex.axis = 0.9, las=1) text(expand.grid(1:dim, 1:dim), sprintf("%%0.2f", dst), cex=0.6) dev.off() """ % ffr(self.pathout['labbe-matrix.png']) + txt += """ + library(igraph) + g <- graph.adjacency(as.matrix(1-dist.mat), mode="lower", weighted=T) + write.graph(g, file="%s", format='graphml') + open_file_graph("%s", width=1000, height=1000, svg=F) + plot(g) + dev.off() + E(g)$weight <- 1 - E(g)$weight + g <- minimum.spanning.tree(g) + E(g)$weight <- 1 - E(g)$weight + write.graph(g, file="%s", format='graphml') + open_file_graph("%s", width=1000, height=1000, svg=F) + plot(g) + dev.off() + """ % (ffr(self.pathout['graph_tot.graphml']), ffr(self.pathout['graph_tot.png']), ffr(self.pathout['graph_min.graphml']), ffr(self.pathout['graph_min.png'])) self.add(txt) self.write() @@ -1511,6 +1560,83 @@ class ChronoPropScript(PrintRScript) : self.add(txt) self.write() +class DendroScript(PrintRScript) : + def make_script(self) : + if self.parametres['svg'] : + typefile = '.svg' + else : + typefile = '.png' + fileout = self.parametres['fileout'] + width = self.parametres['width'] + height = self.parametres['height'] + type_dendro = self.parametres['dendro_type'] + if self.parametres['taille_classe'] : + tclasse = 'TRUE' + else : + tclasse = 'FALSE' + if self.parametres['color_nb'] == 0 : + bw = 'FALSE' + else : + bw = 'TRUE' + if self.parametres['type_tclasse'] == 0 : + histo='FALSE' + else : + histo = 'TRUE' + if self.parametres['svg'] : + svg = 'TRUE' + else : + svg = 'FALSE' + dendro_path = self.pathout['Rdendro'] + classe_path = self.pathout['uce'] + txt = """ + library(ape) + load("%s") + source("%s") + classes <- read.csv2("%s", row.names=1) + classes <- classes[,1] + """ % (ffr(dendro_path), ffr(self.parametres['Rgraph']), ffr(classe_path)) + if self.parametres['dendro'] == 'simple' : + txt += """ + open_file_graph("%s", width=%i, height=%i, svg=%s) + plot.dendropr(tree.cut1$tree.cl, classes, type.dendro="%s", histo=%s, bw=%s, lab=NULL, tclasse=%s) + """ % (ffr(fileout), width, height, svg, type_dendro, histo, bw, tclasse) + elif self.parametres['dendro'] == 'texte' : + txt += """ + load("%s") + source("%s") + if (is.null(debsup)) { + debsup <- debet + } + chistable <- chistabletot[1:(debsup-1),] + """ % (ffr(self.pathout['RData.RData']), ffr(self.parametres['Rgraph'])) + if self.parametres.get('translation', False) : + txt += """ + rn <- read.csv2("%s", header=FALSE, sep='\t') + rnchis <- row.names(chistable) + commun <- intersect(rnchis, unique(rn[,2])) + idrnchis <- sapply(commun, function(x) {which(rnchis==x)}) + idrn <- sapply(commun, function(x) {which(as.vector(rn[,2])==x)[1]}) + rownames(chistable)[idrnchis] <- as.vector(rn[idrn,1]) + """ % ffr(self.parametres['translation']) + txt += """ + open_file_graph("%s", width=%i, height=%i, svg = %s) + plot.dendro.prof(tree.cut1$tree.cl, classes, chistable, nbbycl = 60, type.dendro="%s", bw=%s, lab=NULL) + """ % (ffr(fileout), width, height, svg, type_dendro, bw) + elif self.parametres['dendro'] == 'cloud' : + txt += """ + load("%s") + source("%s") + if (is.null(debsup)) { + debsup <- debet + } + chistable <- chistabletot[1:(debsup-1),] + open_file_graph("%s", width=%i, height=%i, svg=%s) + plot.dendro.cloud(tree.cut1$tree.cl, classes, chistable, nbbycl = 300, type.dendro="%s", bw=%s, lab=NULL) + """ % (ffr(self.pathout['RData.RData']), ffr(self.parametres['Rgraph']), ffr(fileout), width, height, svg, type_dendro, bw) + self.add(txt) + self.write() + + class ReDoProfScript(PrintRScript) : def make_script(self) : self.sources([self.analyse.parent.RscriptsPath['chdfunct.R']]) -- 2.7.4