+
+class ProtoScript(PrintRScript) :
+ def make_script(self) :
+ self.sources([self.analyse.parent.RscriptsPath['Rgraph'], self.analyse.parent.RscriptsPath['prototypical.R']])
+ self.packages(['wordcloud'])
+ if self.parametres.get('cloud', False) :
+ cloud = 'TRUE'
+ else :
+ cloud = 'FALSE'
+ txt = """
+ errorn <- function(x) {
+ qnorm(0.975)*sd(x)/sqrt(lenght(n))
+ }
+ errort <- function(x) {
+ qt(0.975,df=lenght(x)-1)*sd(x)/sqrt(lenght(x))
+ }
+ 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')
+ 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)
+ self.write()
+
+
+class ExportAfc(PrintRScript) :
+ def make_script(self) :
+ self.source([self.analyse.parent.RscriptsPath['Rgraph']])
+ self.packages(['rgexf'])
+ txt = """
+ """
+
+class TgenSpecScript(PrintRScript):
+ def make_script(self):
+ self.packages(['textometry'])
+ txt = """
+ tgen <- read.csv2("%s", row.names = 1, sep = '\\t')
+ """ % ffr(self.parametres['tgeneff'])
+ txt += """
+ tot <- tgen[nrow(tgen), ]
+ result <- NULL
+ tgen <- tgen[-nrow(tgen),]
+ for (i in 1:nrow(tgen)) {
+ mat <- rbind(tgen[i,], tot - tgen[i,])
+ specmat <- specificities(mat)
+ result <- rbind(result, specmat[1,])
+ }
+ colnames(result) <- colnames(tgen)
+ row.names(result) <- rownames(tgen)
+ write.table(result, file = "%s", sep='\\t', col.names = NA)
+ """ % 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