+
+
+class ChronoChi2Script(PrintRScript):
+
+ def make_script(self):
+ self.sources([self.analyse.parent.RscriptsPath['Rgraph']])
+ print(self.parametres)
+ txt = """
+ inRData <- "%s"
+ dendrof <- "%s"
+ load(inRData)
+ load(dendrof)
+ """ % (ffr(self.pathout['RData.RData']), ffr(self.pathout['dendrogramme.RData']))
+ txt += """
+ svg <- %s
+ """ % self.parametres['svg']
+ txt += """
+ tc <- which(grepl("%s",rownames(chistabletot)))
+ rn <- rownames(chistabletot)[tc]
+ tc <- tc[order(rn)]
+ dpt <- chistabletot[tc,]
+ tot <- afctable[tc,]
+ tcp <- rowSums(tot)
+ ptc <- tcp/sum(tcp)
+ dpt <- t(dpt)
+ dd <- dpt
+ """ % self.parametres['var'].replace('*', "\\\\*")
+ txt += """
+ classes <- n1[,ncol(n1)]
+ tcl <- table(classes)
+ if ('0' %in% names(tcl)) {
+ to.vire <- which(names(tcl) == '0')
+ tcl <- tcl[-to.vire]
+ }
+ tclp <- tcl/sum(tcl)
+ #chi2 colors
+ library(ape)
+ k <- 1e-02
+ lcol <- NULL
+ lk <- k
+ for (i in 1:5) {
+ lcol <- c(lcol, qchisq(1-k,1))
+ k <- k/10
+ lk <- c(lk,k)
+ }
+ lcol <- c(3.84, lcol)
+ lcol <- c(-Inf,lcol)
+ lcol <- c(lcol, Inf)
+ lk <- c(0.05,lk)
+ breaks <- lcol
+ alphas <- seq(0,1, length.out=length(breaks))
+ clod <- rev(as.numeric(tree.cut1$tree.cl$tip.label))
+ #end
+ """
+ txt += """
+ open_file_graph("%s", w=%i, h=%i, svg=svg)
+ """ % (ffr(self.parametres['tmpgraph']), self.parametres['width'], self.parametres['height'])
+ txt += """
+ par(mar=c(3,3,3,3))
+ mat.graphic <- matrix(c(rep(1,nrow(dd)),c(2:(nrow(dd)+1))), ncol=2)
+ mat.graphic <- rbind(mat.graphic, c(max(mat.graphic) + 1 , max(mat.graphic) + 2))
+ hauteur <- tclp[clod] * 0.9
+ heights.graphic <- append(hauteur, 0.1)
+ layout(mat.graphic, heights=heights.graphic, widths=c(0.15,0.85))
+ par(mar=c(0,0,0,0))
+ tree.toplot <- tree.cut1$tree.cl
+ num.label <- as.numeric(tree.cut1$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))
+ lcol <- cut(dd[i,], breaks, include.lowest=TRUE)
+ ulcol <- names(table(lcol))
+ lcol <- as.character(lcol)
+ for (j in 1:length(ulcol)) {
+ lcol[which(lcol==ulcol[j])] <- j
+ }
+ lcol <- as.numeric(lcol)
+ mcol <- rainbow(nrow(dd))[i]
+ last.col <- NULL
+ for (k in alphas) {
+ last.col <- c(last.col, rgb(r=col2rgb(mcol)[1]/255, g=col2rgb(mcol)[2]/255, b=col2rgb(mcol)[3]/255, a=k))
+ }
+ #print(last.col)
+ barplot(rep(1,ncol(dd)), width=ptc, names.arg=FALSE, axes=FALSE, col=last.col[lcol], border=rgb(r=0, g=0, b=0, a=0.3))
+ }
+ plot(0,type='n',axes=FALSE,ann=FALSE)
+ label.coords <- barplot(rep(1, ncol(dd)), width=ptc, names.arg = F, las=2, axes=F, ylim=c(0,1), plot=T, col='white')
+ text(x=label.coords, y=0.5, labels=rn[order(rn)], srt=90)
+ dev.off()
+ """
+ self.add(txt)
+ self.write()
+
+
+class ChronoPropScript(PrintRScript):
+
+ def make_script(self):
+ self.sources([self.analyse.parent.RscriptsPath['Rgraph']])
+ print(self.parametres)
+ txt = """
+ inRData <- "%s"
+ dendrof <- "%s"
+ load(inRData)
+ load(dendrof)
+ """ % (ffr(self.pathout['RData.RData']), ffr(self.pathout['dendrogramme.RData']))
+ txt += """
+ svg <- %s
+ """ % self.parametres['svg']
+ txt += """
+ tc <- which(grepl("%s",rownames(chistabletot)))
+ rn <- rownames(chistabletot)[tc]
+ tc <- tc[order(rn)]
+ dpt <- chistabletot[tc,]
+ tot <- afctable[tc,]
+ tcp <- rowSums(tot)
+ ptc <- tcp/sum(tcp)
+ dpt <- t(dpt)
+ dd <- dpt
+ """ % self.parametres['var'].replace('*', "\\\\*")
+ txt += """
+ classes <- n1[,ncol(n1)]
+ tcl <- table(classes)
+ if ('0' %in% names(tcl)) {
+ to.vire <- which(names(tcl) == '0')
+ tcl <- tcl[-to.vire]
+ }
+ tclp <- tcl/sum(tcl)
+ """
+ txt += """
+ open_file_graph("%s", w=%i, h=%i, svg=svg)
+ """ % (ffr(self.parametres['tmpgraph']), self.parametres['width'], self.parametres['height'])
+ txt+= """
+ ptt <- prop.table(as.matrix(tot), 1)
+ par(mar=c(10,2,2,2))
+ barplot(t(ptt)[as.numeric(tree.cut1$tree.cl$tip.label),], col=rainbow(ncol(ptt))[as.numeric(tree.cut1$tree.cl$tip.label)], width=ptc, las=3, space=0.05, cex.axis=0.7, border=NA)
+ dev.off()
+ """
+ self.add(txt)
+ self.write()
+
+
+class ChronoggScript(PrintRScript):
+
+ def make_script(self):
+ self.sources([self.analyse.parent.RscriptsPath['Rgraph']])
+ print(self.parametres)
+ txt = """
+ library(ggplot2)
+ inRData <- "%s"
+ dendrof <- "%s"
+ load(inRData)
+ load(dendrof)
+ """ % (ffr(self.pathout['RData.RData']), ffr(self.pathout['dendrogramme.RData']))
+ txt += """
+ svg <- %s
+ """ % self.parametres['svg']
+ txt += """
+ tc <- which(grepl("%s",rownames(chistabletot)))
+ rn <- rownames(chistabletot)[tc]
+ tc <- tc[order(rn)]
+ dpt <- chistabletot[tc,]
+ tot <- afctable[tc,]
+ tcp <- rowSums(tot)
+ ptc <- tcp/sum(tcp)
+ dpt <- t(dpt)
+ dd <- dpt
+ """ % self.parametres['var'].replace('*', "\\\\*")
+ txt += """
+ classes <- n1[,ncol(n1)]
+ tcl <- table(classes)
+ if ('0' %in% names(tcl)) {
+ to.vire <- which(names(tcl) == '0')
+ tcl <- tcl[-to.vire]
+ }
+ tclp <- tcl/sum(tcl)
+ ptt <- prop.table(as.matrix(tot), 1)
+ ptt <- ptt[,as.numeric(tree.cut1$tree.cl$tip.label)]
+ rownames(ptt) <- cumsum(ptc)
+ nptt<-as.data.frame(as.table(ptt))
+ nptt[,1]<-as.numeric(as.character(nptt[,1]))
+ col <- rainbow(ncol(ptt))[as.numeric(tree.cut1$tree.cl$tip.label)]
+ """
+ txt += """
+ open_file_graph("%s", w=%i, h=%i, svg=svg)
+ """ % (ffr(self.parametres['tmpgraph']), self.parametres['width'], self.parametres['height'])
+ txt+= """
+ par(mar=c(10,2,2,2))
+ gg <- ggplot(data=nptt, aes(x=Var1,y=Freq,fill=Var2)) + geom_area(alpha=1 , size=0.5, colour="black")
+ gg + scale_fill_manual(values=col)
+ dev.off()
+ """
+ self.add(txt)
+ self.write()
+
+
+class DendroScript(PrintRScript):
+
+ def make_script(self):
+ if self.parametres['svg']:
+ typefile = '.svg'
+ else:
+ typefile = '.png'
+ fileout = self.parametres['fileout']
+ width = self.parametres['width']
+ height = self.parametres['height']
+ type_dendro = self.parametres['dendro_type']
+ if self.parametres['taille_classe']:
+ tclasse = 'TRUE'
+ else:
+ tclasse = 'FALSE'
+ if self.parametres['color_nb'] == 0:
+ bw = 'FALSE'
+ else:
+ bw = 'TRUE'
+ if self.parametres['type_tclasse'] == 0:
+ histo='FALSE'
+ else:
+ histo = 'TRUE'
+ if self.parametres['svg']:
+ svg = 'TRUE'
+ else:
+ svg = 'FALSE'
+ dendro_path = self.pathout['Rdendro']
+ classe_path = self.pathout['uce']
+ txt = """
+ library(ape)
+ load("%s")
+ source("%s")
+ classes <- read.csv2("%s", row.names=1)
+ classes <- classes[,1]
+ """ % (ffr(dendro_path), ffr(self.parametres['Rgraph']), ffr(classe_path))
+ if self.parametres['dendro'] == 'simple':
+ txt += """
+ open_file_graph("%s", width=%i, height=%i, svg=%s)
+ plot.dendropr(tree.cut1$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']])
+ print(self.parametres)