# -*- coding: utf-8 -*-
#Author: Pierre Ratinaud
#Copyright (c) 2008-2011 Pierre Ratinaud
-#Lisense: GNU/GPL
+#License: GNU/GPL
import tempfile
from chemins import ffr
self.analyse = analyse
self.parametres = analyse.parametres
self.scriptout = self.pathout['temp']
- self.script = u"#Script genere par IRaMuTeQ - %s" % datetime.now().ctime()
+ self.script = u"#Script genere par IRaMuTeQ - %s\n" % datetime.now().ctime()
def add(self, txt) :
self.script = '\n'.join([self.script, txt])
def sources(self, lsources) :
for source in lsources :
- self.add('source("%s")' % source)
+ self.add('source("%s", encoding = \'utf8\')' % source)
def packages(self, lpks) :
for pk in lpks :
fileout.close()
def RPamTxt(corpus, RscriptPath):
- DicoPath = corpus.dictpathout
- param = corpus.parametre
- print param
+ DicoPath = corpus.pathout
+ param = corpus.parametres
txt = """
source("%s")
""" % (RscriptPath['pamtxt'])
save(tree.cut1, file="%s")
open_file_graph("%s", width = 600, height=400)
classes<-n1[,ncol(n1)]
- plot.dendropr(tree_cut1$tree.cl,classes)
+ plot.dendropr(tree_cut1$tree.cl,classes, histo = TRUE)
""" % (DicoPath['Rdendro'],DicoPath['dendro1'])
txt += """
""" % (DictChdTxtOut['afc_facteur'], DictChdTxtOut['afc_col'], DictChdTxtOut['afc_row'])
txt += """
- #xlab <- paste('facteur 1 - ', round(afc$facteur[1,2],2), sep = '')
- #ylab <- paste('facteur 2 - ', round(afc$facteur[2,2],2), sep = '')
- #xlab <- paste(xlab, ' %', sep = '')
- #ylab <- paste(ylab, ' %', sep = '')
- """
-
- txt += """
PARCEX<-%s
- xmin <- min(afc$rowcoord[,1], na.rm = TRUE) + (0.1 * min(afc$rowcoord[,1], na.rm = TRUE))
- xmax <- max(afc$rowcoord[,1], na.rm = TRUE) + (0.1 * max(afc$rowcoord[,1], na.rm = TRUE))
- ymin <- min(afc$rowcoord[,2], na.rm = TRUE) + (0.1 * min(afc$rowcoord[,2], na.rm = TRUE))
- ymax <- max(afc$rowcoord[,2], na.rm = TRUE) + (0.1 * max(afc$rowcoord[,2], na.rm = TRUE))
- print(xmin)
- print(xmax)
- print(ymin)
- print(ymax)
""" % taillecar
txt += """
- PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", what='coord', deb=1, fin=(debsup-1), xlab = xlab, ylab = ylab, xmin=xmin, xmax=xmax, ymin = ymin, ymax=ymax)
+ xyminmax <- PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", what='coord', deb=1, fin=(debsup-1), xlab = xlab, ylab = ylab)
""" % (DictChdTxtOut['AFC2DL_OUT'])
txt += """
- PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", what='coord', deb=debsup, fin=(debet-1), xlab = xlab, ylab = ylab, xmin=xmin, xmax=xmax, ymin = ymin, ymax=ymax)
+ PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", what='coord', deb=debsup, fin=(debet-1), xlab = xlab, ylab = ylab, xmin = xyminmax$xminmax[1], xmax = xyminmax$xminmax[2], ymin = xyminmax$yminmax[1], ymax = xyminmax$yminmax[2], active=FALSE)
""" % (DictChdTxtOut['AFC2DSL_OUT'])
txt += """
- PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", what='coord', deb=debet, fin=fin, xlab = xlab, ylab = ylab, xmin=xmin, xmax=xmax, ymin = ymin, ymax=ymax)
+ if ((fin - debet) > 2) {
+ PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", what='coord', deb=debet, fin=fin, xlab = xlab, ylab = ylab, xmin = xyminmax$xminmax[1], xmax = xyminmax$xminmax[2], ymin = xyminmax$yminmax[1], ymax = xyminmax$yminmax[2], active = FALSE)
+ }
""" % (DictChdTxtOut['AFC2DEL_OUT'])
txt += """
- PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", col=TRUE, what='coord', xlab = xlab, ylab = ylab, xmin=xmin, xmax=xmax, ymin = ymin, ymax=ymax)
+ PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", col=TRUE, what='coord', xlab = xlab, ylab = ylab, xmin = xyminmax$xminmax[1], xmax = xyminmax$xminmax[2], ymin = xyminmax$yminmax[1], ymax = xyminmax$yminmax[2], active=FALSE)
""" % (DictChdTxtOut['AFC2DCL_OUT'])
# txt += """
# PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", what='crl', deb=1, fin=(debsup-1), xlab = xlab, ylab = ylab)
# height = 400
rownames = 'c("' + '","'.join(rownames) + '")'
colnames = 'c("' + '","'.join(colnames) + '")'
+
if not intxt :
#FIXME
txt = """
self.packages(['igraph', 'proxy', 'Matrix'])
self.sources([self.analyse.parent.RscriptsPath['simi'], self.analyse.parent.RscriptsPath['Rgraph']])
txt = ''
- if not self.parametres['keep_coord'] :
+ if not self.parametres['keep_coord'] and not self.parametres['type'] == 'simimatrix':
txt += """
dm.path <- "%s"
cn.path <- "%s"
dm <-readMM(dm.path)
cn <- read.table(cn.path, sep='\t', quote='"')
colnames(dm) <- cn[,1]
- sel.col <- read.csv2(selected.col, header = FALSE)
- sel.col <- sel.col[,1] + 1
+ if (file.exists(selected.col)) {
+ sel.col <- read.csv2(selected.col, header = FALSE)
+ sel.col <- sel.col[,1] + 1
+ } else {
+ sel.col <- 1:ncol(dm)
+ }
+ if (!word) {
+ dm <- dm[, sel.col]
+ } else {
+ forme <- colnames(dm)[index]
+ if (!index %in% sel.col) {
+ sel.col <- append(sel.col, index)
+ }
+ dm <- dm[, sel.col]
+ index <- which(colnames(dm) == forme)
+ }
+ """
+ elif not self.parametres['keep_coord'] and self.parametres['type'] == 'simimatrix' :
+ txt += """
+ dm.path <- "%s"
+ selected.col <- "%s"
+ """ % (self.pathout['mat01.csv'], self.pathout['selected.csv'])
+ if 'word' in self.parametres :
+ txt += """
+ word <- TRUE
+ index <- %i + 1
+ """ % self.parametres['word']
+ else :
+ txt += """
+ word <- FALSE
+ """
+ txt += """
+ dm <-read.csv2(dm.path)
+ dm <- as.matrix(dm)
+ if (file.exists(selected.col)) {
+ sel.col <- read.csv2(selected.col, header = FALSE)
+ sel.col <- sel.col[,1] + 1
+ } else {
+ sel.col <- 1:ncol(dm)
+ }
if (!word) {
dm <- dm[, sel.col]
} else {
index <- which(colnames(dm) == forme)
}
"""
-
else :
txt += """
load("%s")
txt += """
mat <- as.matrix(stats::as.dist(mat,diag=TRUE,upper=TRUE))
mat[is.na(mat)] <- 0
- mat[is.infinite(mat)] <- 0
+ if (length(which(mat == Inf))) {
+ infp <- which(mat == Inf)
+ mat[infp] <- NA
+ maxmat <- max(mat, na.rm = TRUE)
+ if (maxmat > 0) {
+ maxmat <- maxmat + 1
+ } else {
+ maxmat <- 0
+ }
+ mat[infp] <- maxmat
+ }
+ if (length(which(mat == -Inf))) {
+ infm <- which(mat == -Inf)
+ mat[infm] <- NA
+ minmat <- min(mat, na.rm = TRUE)
+ if (maxmat < 0) {
+ minmat <- minmat - 1
+ } else {
+ minmat <- 0
+ }
+ mat[infm] <- minmat
+ }
"""
if 'word' in self.parametres and not self.parametres['keep_coord'] :
txt += """
graphnb +=1
self.filename = ffr(os.path.join(dirout,'graph_simi_'+str(graphnb)+'.png'))
if self.parametres['type_graph'] == 2 : type = 'rgl'
+ if self.parametres['type_graph'] == 3 :
+ graphnb = 1
+ type = 'web'
+ dirout = os.path.dirname(self.pathout['mat01'])
+ 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)
+ self.filename = os.path.join(self.filename, 'gexf.gexf')
+ if self.parametres['type_graph'] == 4 :
+ graphnb = 1
+ type = 'rglweb'
+ dirout = os.path.dirname(self.pathout['mat01'])
+ while os.path.exists(os.path.join(dirout,'webrgl_'+str(graphnb))):
+ graphnb +=1
+ self.filename = ffr(os.path.join(dirout,'webrgl_'+str(graphnb)))
+ os.mkdir(self.filename)
if self.parametres['arbremax'] :
arbremax = 'TRUE'
# g.toplot <- g.ori
# }
# """
+ if self.parametres['com'] :
+ com = `self.parametres['communities']`
+ else :
+ com = 'NULL'
+ if self.parametres['halo'] :
+ halo = 'TRUE'
+ else :
+ halo = 'FALSE'
+ txt += """
+ communities <- %s
+ halo <- %s
+ """ % (com, halo)
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)
+ 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)
""" % (method, type, layout, arbremax, coeff_tv, coeff_te)
if self.parametres.get('bystar',False) :
"""
else :
txt+="""
- label.cex <- NULL
+ label.cex <- cex
"""
if self.parametres.get('sfromchi', False) :
txt += """
vertex.size <- NULL
"""
else :
- if self.parametres['type'] == 'clustersimitxt' :
+ #print self.parametres
+ if (self.parametres['type'] == 'clustersimitxt' and self.parametres.get('tmpchi', False)) or (self.parametres['type'] == 'simimatrix' and 'tmpchi' in self.parametres):
txt += """
lchi <- read.table("%s")
lchi <- lchi[,1]
else :
txt += """
if (is.null(vcexminmax[1])) {
- label.cex <- NULL
+ label.cex <- cex
} else {
label.cex <- graph.simi$label.cex
}
"""
- if self.parametres['type'] == 'clustersimitxt' and self.parametres.get('sfromchi', False) :
+ if (self.parametres['type'] == 'clustersimitxt' or self.parametres['type'] == 'simimatrix') and self.parametres.get('sfromchi', False):
txt += """
vertex.size <- norm.vec(lchi, minmaxeff[1], minmaxeff[2])
+ if (!length(vertex.size)) vertex.size <- 0
"""
else :
txt += """
if (is.null(minmaxeff[1])) {
- vertex.size <- NULL
+ vertex.size <- 0
} else {
vertex.size <- graph.simi$eff
}
"""
- txt += """ vertex.size <- NULL """
+ #txt += """ vertex.size <- NULL """
+ if self.parametres['svg'] : svg = 'TRUE'
+ else : svg = 'FALSE'
+ txt += """
+ svg <- %s
+ """ % svg
txt += """
- coords <- plot.simi(graph.simi, p.type='%s',filename="%s", vertex.label = label.v, edge.label = label.e, vertex.col = cols, 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)
+ vertex.col <- cols
+ if (!is.null(graph.simi$com)) {
+ com <- graph.simi$com
+ colm <- rainbow(length(com))
+ if (vertex.size != 0 || graph.simi$halo) {
+ vertex.label.color <- 'black'
+ vertex.col <- colm[membership(com)]
+ } else {
+ 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)
save.image(file="%s")
""" % (type, self.filename, self.pathout['RData'])
self.packages(['wordcloud'])
bg_col = Rcolor(self.parametres['col_bg'])
txt_col = Rcolor(self.parametres['col_text'])
+ if self.parametres['svg'] :
+ svg = 'TRUE'
+ else :
+ svg = 'FALSE'
txt = """
+ svg <- %s
+ """ % svg
+ txt += """
act <- read.csv2("%s", header = FALSE, row.names=1, sep='\t')
selected.col <- read.table("%s")
toprint <- as.matrix(act[selected.col[,1] + 1,])
toprint <- as.matrix(toprint[order(toprint[,1], decreasing=TRUE),])
toprint <- as.matrix(toprint[1:maxword,])
}
- open_file_graph("%s", width = %i, height = %i)
+ open_file_graph("%s", width = %i, height = %i , svg = svg)
par(bg=rgb%s)
wordcloud(row.names(toprint), toprint[,1], scale=c(%f,%f), random.order=FALSE, colors=rgb%s)
dev.off()
""" % (ffr(self.analyse.pathout['actives_eff.csv']), ffr(self.analyse.pathout['selected.csv']), self.parametres['maxword'], ffr(self.parametres['graphout']), self.parametres['width'], self.parametres['height'], bg_col, self.parametres['maxcex'], self.parametres['mincex'], txt_col)
self.add(txt)
self.write()
+
+class ProtoScript(PrintRScript) :
+ def make_script(self) :
+ self.sources([self.analyse.parent.RscriptsPath['Rgraph'], self.analyse.parent.RscriptsPath['prototypical.R']])
+ self.packages(['wordcloud'])
+ txt = """
+ 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))
+ dev.off()
+ """ % (self.analyse.pathout['table.csv'], self.analyse.pathout['proto.png'], self.parametres['limfreq'], self.parametres['limrang'])
+ self.add(txt)
+ self.write()
+
+
+class ExportAfc(PrintRScript) :
+ def make_script(self) :
+ self.source([self.analyse.parent.RscriptsPath['Rgraph']])
+ self.packages(['rgexf'])
+ txt = """
+ """
+