X-Git-Url: http://iramuteq.org/git?p=iramuteq;a=blobdiff_plain;f=PrintRScript.py;h=deaddf51ced131c513700e1eda655a5e86b25a58;hp=8e54bf42bcfc315eb0b92648fd8dbd39aa4c02c4;hb=3d1a621b481e251f8a086af586c7eb0bb87b0004;hpb=b02f2cba3d8c7dba29a54de8b589626d008d2c5b diff --git a/PrintRScript.py b/PrintRScript.py index 8e54bf4..deaddf5 100644 --- a/PrintRScript.py +++ b/PrintRScript.py @@ -319,7 +319,7 @@ def RchdQuest(DicoPath, RscriptPath, nbcl = 10, mincl = 10): fileout.write(txt) fileout.close() -def AlcesteTxtProf(DictChdTxtOut, RscriptsPath, clnb, taillecar): +def ReinertTxtProf(DictChdTxtOut, RscriptsPath, clnb, taillecar): txt = "clnb<-%i\n" % clnb txt += """ source("%s") @@ -704,7 +704,7 @@ class PrintSimiScript(PrintRScript) : self.packages(['igraph', 'proxy', 'Matrix']) self.sources([self.analyse.parent.RscriptsPath['simi'], self.analyse.parent.RscriptsPath['Rgraph']]) txt = '' - if not self.parametres['keep_coord'] and not self.parametres['type'] == 'simimatrix': + if not self.parametres['keep_coord'] and not (self.parametres['type'] == 'simimatrix' or self.parametres['type'] == 'simiclustermatrix') : txt += """ dm.path <- "%s" cn.path <- "%s" @@ -740,7 +740,7 @@ class PrintSimiScript(PrintRScript) : index <- which(colnames(dm) == forme) } """ - elif not self.parametres['keep_coord'] and self.parametres['type'] == 'simimatrix' : + elif not self.parametres['keep_coord'] and (self.parametres['type'] == 'simimatrix' or self.parametres['type'] == 'simiclustermatrix'): txt += """ dm.path <- "%s" selected.col <- "%s" @@ -909,7 +909,16 @@ class PrintSimiScript(PrintRScript) : if self.parametres['seuil_ok'] : seuil = str(self.parametres['seuil']) else : seuil = 'NULL' - + + if not self.parametres.get('edgecurved', False) : + ec = 'FALSE' + else : + ec = 'TRUE' + + txt += """ + edge.curved <- %s + """ % ec + cols = str(self.parametres['cols']).replace(')',', max=255)') cola = str(self.parametres['cola']).replace(')',',max=255)') @@ -1072,7 +1081,7 @@ class PrintSimiScript(PrintRScript) : """ else : #print self.parametres - if (self.parametres['type'] == 'clustersimitxt' and self.parametres.get('tmpchi', False)) or (self.parametres['type'] == 'simimatrix' and 'tmpchi' in self.parametres): + if (self.parametres['type'] == 'clustersimitxt' and self.parametres.get('tmpchi', False)) or (self.parametres['type'] in ['simimatrix','simiclustermatrix'] and 'tmpchi' in self.parametres): txt += """ lchi <- read.table("%s") lchi <- lchi[,1] @@ -1080,7 +1089,7 @@ class PrintSimiScript(PrintRScript) : txt += """ lchi <- lchi[sel.col] """ - if self.parametres['type'] == 'clustersimitxt' and self.parametres.get('cexfromchi', False) : + if self.parametres['type'] in ['clustersimitxt', 'simimatrix', 'simiclustermatrix'] and self.parametres.get('cexfromchi', False) : txt += """ label.cex <- norm.vec(lchi, vcexminmax[1], vcexminmax[2]) """ @@ -1092,7 +1101,7 @@ class PrintSimiScript(PrintRScript) : label.cex <- graph.simi$label.cex } """ - if (self.parametres['type'] == 'clustersimitxt' or self.parametres['type'] == 'simimatrix') and self.parametres.get('sfromchi', False): + if (self.parametres['type'] in ['clustersimitxt', 'simimatrix', 'simiclustermatrix']) and self.parametres.get('sfromchi', False): txt += """ vertex.size <- norm.vec(lchi, minmaxeff[1], minmaxeff[2]) if (!length(vertex.size)) vertex.size <- 0 @@ -1123,7 +1132,7 @@ class PrintSimiScript(PrintRScript) : vertex.label.color <- colm[membership(com)] } } - coords <- plot.simi(graph.simi, p.type='%s',filename="%s", vertex.label = label.v, edge.label = label.e, vertex.col = vertex.col, vertex.label.color = vertex.label.color, vertex.label.cex=label.cex, vertex.size = vertex.size, edge.col = cola, leg=leg, width = width, height = height, alpha = alpha, movie = film, svg = svg) + coords <- plot.simi(graph.simi, p.type='%s',filename="%s", vertex.label = label.v, edge.label = label.e, vertex.col = vertex.col, vertex.label.color = vertex.label.color, vertex.label.cex=label.cex, vertex.size = vertex.size, edge.col = cola, leg=leg, width = width, height = height, alpha = alpha, movie = film, edge.curved = edge.curved, svg = svg) save.image(file="%s") """ % (type, self.filename, ffr(self.pathout['RData'])) @@ -1210,6 +1219,44 @@ class TgenSpecScript(PrintRScript): colnames(result) <- colnames(tgen) row.names(result) <- rownames(tgen) write.table(result, file = "%s", sep='\\t', col.names = NA) - """ % self.pathout['tgenspec.csv'] + """ % ffr(self.pathout['tgenspec.csv']) self.add(txt) +class TgenProfScript(PrintRScript): + def make_script(self): + self.sources([self.analyse.ira.RscriptsPath['chdfunct']]) + txt = """ + tgen <- read.csv2("%s", row.names = 1, sep = '\\t') + """ % ffr(self.parametres['tgeneff']) + txt += """ + res <- build.prof.tgen(tgen) + write.table(res$chi2, file = "%s", sep='\\t', col.names = NA) + write.table(res$pchi2, file = "%s", sep='\\t', col.names = NA) + """ % (ffr(self.pathout['tgenchi2.csv']), ffr(self.pathout['tgenpchi2.csv'])) + self.add(txt) + +class FreqMultiScript(PrintRScript): + def make_script(self): + self.sources([self.analyse.parent.RscriptsPath['Rgraph']]) + txt = """ + freq <- read.csv2("%s", row.names=1, sep='\\t', dec='.') + """ % ffr(self.pathout['frequences.csv']) + txt += """ + toplot <- freq[order(freq[,2]) ,2] + toplot.names = rownames(freq)[order(freq[,2])] + h <- 80 + (20 * nrow(freq)) + open_file_graph("%s",height=h, width=500) + par(mar=c(3,20,3,3)) + barplot(toplot, names = toplot.names, horiz=TRUE, las =1, col = rainbow(nrow(freq))) + dev.off() + """ % ffr(self.pathout['barplotfreq.png']) + txt += """ + toplot <- freq[order(freq[,4]) ,4] + toplot.names = rownames(freq)[order(freq[,4])] + open_file_graph("%s",height=h, width=500) + par(mar=c(3,20,3,3)) + barplot(toplot, names = toplot.names, horiz=TRUE, las =1, col = rainbow(nrow(freq))) + dev.off() + """ % ffr(self.pathout['barplotrow.png']) + self.add(txt) + self.write() \ No newline at end of file