if self.parametres['film'] :
txt += """
film <- "%s"
- """ % self.pathout['film']
+ """ % ffr(self.pathout['film'])
else :
txt += """
film <- NULL
"""
class MergeGraphes(PrintRScript) :
- def __init__(self, parametres):
+ def __init__(self, analyse):
self.script = u"#Script genere par IRaMuTeQ - %s\n" % datetime.now().ctime()
self.pathout = PathOut()
- self.parametres = parametres
+ self.parametres = analyse.parametres
self.scriptout = self.pathout['temp']
+ self.analyse = analyse
def make_script(self) :
#FIXME
V(g)$weight <- (graph.simi$mat.eff/nrow(dm))*100
graphs[['%s']] <- g
"""
- for i, graph in enumerate(self.parametres['lgraphes']) :
+ for i, graph in enumerate(self.parametres['graphs']) :
path = os.path.dirname(graph)
gname = ''.join(['g', `i`])
RData = os.path.join(path,'RData.RData')
self.add(txt)
self.write()
+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)
+ """ % (self.pathout['RData.RData'], 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']
+ 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$tree.cl
+ tree.toplot$tip.label <- paste('classe ', tree.toplot$tip.label)
+ plot.phylo(tree.toplot,label.offset=0.1, cex=1.1, no.margin=T)
+ 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)
+ """ % (self.pathout['RData.RData'], 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']
+ 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()
+
import wx.lib.mixins.listctrl as listmix
from listlex import ListForSpec
from chemins import ConstructPathOut, ffr
-from dialog import PrefUCECarac, SearchDial, message, BarFrame
+from dialog import PrefUCECarac, SearchDial, message, BarFrame, ChronoFrame
from tableau import copymatrix
from search_tools import SearchFrame
import webbrowser
self.attr2 = wx.ListItemAttr()
self.attr2.SetBackgroundColour((190, 249, 236))
self.attr2s = wx.ListItemAttr()
- self.attr2s.SetBackgroundColour((211, 252, 244))
+ self.attr2s.SetBackgroundColour((211, 252, 244))
self.attr3 = wx.ListItemAttr()
self.attr3.SetBackgroundColour((245, 180, 180))
self.attr3s = wx.ListItemAttr()
self.InsertColumn(5, "Type", wx.LIST_FORMAT_RIGHT)
self.InsertColumn(6, "forme", wx.LIST_FORMAT_RIGHT)
self.InsertColumn(7, "p", wx.LIST_FORMAT_RIGHT)
-
+
self.SetColumnWidth(0, 60)
self.SetColumnWidth(1, 70)
self.itemDataMap = dictdata
self.itemIndexMap = dictdata.keys()
self.SetItemCount(len(dictdata))
-
+
#mixins
listmix.ListCtrlAutoWidthMixin.__init__(self)
listmix.ColumnSorterMixin.__init__(self, len(classen[0]))
items = list(self.itemDataMap.keys())
items.sort(sorter)
self.itemIndexMap = items
-
+
# redraw the list
self.Refresh()
self.idexporttropes = wx.NewId()
self.idexportowledge = wx.NewId()
self.onmaketgen = wx.NewId()
+ self.onchronochi2 = wx.NewId()
+ self.onchronoprop = wx.NewId()
# self.export_classes = wx.NewId()
self.Bind(wx.EVT_MENU, self.OnPopupOne, id=self.popupID1)
self.Bind(wx.EVT_MENU, self.onexporttropes, id = self.idexporttropes)
self.Bind(wx.EVT_MENU, self.onexportowledge, id = self.idexportowledge)
self.Bind(wx.EVT_MENU, self.OnMakeTgen, id=self.onmaketgen)
+ self.Bind(wx.EVT_MENU, self.OnChronoChi2, id=self.onchronochi2)
+ self.Bind(wx.EVT_MENU, self.OnChronoProp, id=self.onchronoprop)
# self.Bind(wx.EVT_MENU, self.on_export_classes, id = self.export_classes)
# self.Bind(wx.EVT_MENU, self.OnPopupThree, id=self.popupID3)
menu.Append(self.idtablex, _(u"Chi2 by cluster").decode('utf8'))
menu.Append(self.idlexdendro, _(u"Chi2 by cluster on dendrogram").decode('utf8'))
menu.Append(self.idchimod, _(u"Chi2 modalities of variable").decode('utf8'))
+ menu_chrono = wx.Menu()
+ menu_chrono.Append(self.onchronochi2, _(u'Chi2').decode('utf8'))
+ menu_chrono.Append(self.onchronoprop, _(u'Proportion').decode('utf8'))
+ menu.AppendMenu(-1, _(u"Chronological view").decode('utf8'), menu_chrono)
menu.Append(self.idwordgraph, _(u"Word graph").decode('utf8'))
#menu.Append(self.export_classes, u"Exporter le corpus...")
-
+
#menu.Append(self.popupID10, u"Spécificités")
menu_conc = wx.Menu()
menu_conc.Append(self.popupID4, _(u"In all segments").decode('utf8'))
menu.AppendMenu(-1, _(u"Concordance").decode('utf8'), menu_conc)
menu.Append(self.onmaketgen, _(u"Make Tgen").decode('utf8'))
- menu_cnrtl = wx.Menu()
+ menu_cnrtl = wx.Menu()
menu_cnrtl.Append(self.popupID5, _(u"Definition").decode('utf8'))
menu_cnrtl.Append(self.popupID6, _(u"Etymology").decode('utf8'))
menu_cnrtl.Append(self.popupID7, _(u"Synonymous").decode('utf8'))
menu.Append(self.idexportowledge, _('Exporter for Owledge').decode('utf8'))
#menu.Append(self.popupID2, u"Concordancier")
# menu.Append(self.popupID3, "recharger")
-
+
self.PopupMenu(menu)
menu.Destroy()
elif 'tableau' in dir(self.Source) :
dial = wx.MessageDialog(self, self.Source.pathout['classe_%i_export.txt' % self.cl], u"Export", wx.OK|wx.ICON_INFORMATION)
dial.ShowModal()
dial.Destroy()
-
+
def onexporttropes(self, evt) :
if 'corpus' in dir(self.Source):
corpus = self.Source.corpus
uci = True
fileout = self.Source.pathout['export_tropes_classe_%i.txt' % self.cl]
corpus.export_tropes(fileout, self.cl, uci = uci)
-
+
def onexportowledge(self, evt):
if 'corpus' in dir(self.Source):
corpus = self.Source.corpus
repout = self.Source.pathout['export_owledge_classe_%i' % self.cl]
if not os.path.exists(repout) :
os.mkdir(repout)
- corpus.export_owledge(repout, self.cl, uci = uci)
+ corpus.export_owledge(repout, self.cl, uci = uci)
def getselectedwords(self) :
words = [self.getColumnText(self.GetFirstSelected(), 6)]
words.append(self.getColumnText(last, 6))
return words
- def quest_var_mod(self, evt) :
+ def quest_var_mod(self, evt) :
word = self.getselectedwords()[0]
if len(word.split('_')) <= 1 :
dial = wx.MessageDialog(self, _(u"This is not a variable_modality form").decode('utf8'), _(u"Problem").decode('utf8'), wx.OK | wx.ICON_WARNING)
dial.ShowModal()
dial.Destroy()
return
-
+
if 'corpus' in dir(self.Source):
corpus = self.Source.corpus
if word.startswith(u'-*') :
dial.CenterOnParent()
dial.ShowModal()
dial.Destroy()
- return
+ return
words.sort()
tableout = []
kwords = []
kwords.append(word)
BarFrame(self.Source.parent, tableout, title, kwords)
+ def OnChronoChi2(self, evt) :
+ word = self.getselectedwords()[0]
+ if len(word.split('_')) <= 1 :
+ dial = wx.MessageDialog(self, _(u"This is not a variable_modality form").decode('utf8'), _(u"Problem").decode('utf8'), wx.OK | wx.ICON_WARNING)
+ dial.CenterOnParent()
+ dial.ShowModal()
+ dial.Destroy()
+ return
+
+ if 'corpus' in dir(self.Source):
+ corpus = self.Source.corpus
+ if word.startswith(u'-*') :
+ if self.them_mod == {} :
+ self.them_mod = self.Source.corpus.make_theme_dict()
+ var_mod = self.them_mod
+ else :
+ if self.var_mod == {} :
+ self.var_mod = self.Source.corpus.make_etoiles_dict()
+ var_mod = self.var_mod
+ else :
+ corpus = self.Source.tableau
+ if self.var_mod == {} :
+ self.var_mod = treat_var_mod([val for val in corpus.actives] + [val for val in corpus.sups])
+ var_mod = self.var_mod
+ var = word.split('_')
+ #words = ['_'.join([var[0],word]) for word in self.var_mod[var[0]]]
+ try :
+ words = [word for word in var_mod[var[0]]]
+ except KeyError:
+ dial = wx.MessageDialog(self, _(u"This is not a meta-data").decode('utf8'), _(u"Problem").decode('utf8'), wx.OK | wx.ICON_WARNING)
+ dial.CenterOnParent()
+ dial.ShowModal()
+ dial.Destroy()
+ return
+ words.sort()
+ vartoplot = var[0] + '_'
+ parametres = {'var' : vartoplot}
+ ChronoFrame(self.Source.parent, parametres, self.Source.pathout, which = 'chi2')
+
+ def OnChronoProp(self, evt) :
+ word = self.getselectedwords()[0]
+ if len(word.split('_')) <= 1 :
+ dial = wx.MessageDialog(self, _(u"This is not a variable_modality form").decode('utf8'), _(u"Problem").decode('utf8'), wx.OK | wx.ICON_WARNING)
+ dial.CenterOnParent()
+ dial.ShowModal()
+ dial.Destroy()
+ return
+
+ if 'corpus' in dir(self.Source):
+ corpus = self.Source.corpus
+ if word.startswith(u'-*') :
+ if self.them_mod == {} :
+ self.them_mod = self.Source.corpus.make_theme_dict()
+ var_mod = self.them_mod
+ else :
+ if self.var_mod == {} :
+ self.var_mod = self.Source.corpus.make_etoiles_dict()
+ var_mod = self.var_mod
+ else :
+ corpus = self.Source.tableau
+ if self.var_mod == {} :
+ self.var_mod = treat_var_mod([val for val in corpus.actives] + [val for val in corpus.sups])
+ var_mod = self.var_mod
+ var = word.split('_')
+ #words = ['_'.join([var[0],word]) for word in self.var_mod[var[0]]]
+ try :
+ words = [word for word in var_mod[var[0]]]
+ except KeyError:
+ dial = wx.MessageDialog(self, _(u"This is not a meta-data").decode('utf8'), _(u"Problem").decode('utf8'), wx.OK | wx.ICON_WARNING)
+ dial.CenterOnParent()
+ dial.ShowModal()
+ dial.Destroy()
+ return
+ words.sort()
+ vartoplot = var[0] + '_'
+ parametres = {'var' : vartoplot}
+ ChronoFrame(self.Source.parent, parametres, self.Source.pathout, which = 'prop')
+
+
def quest_simi(self, evt) :
tableau = self.Source.tableau
tab = tableau.make_table_from_classe(self.cl, self.la)
with open(self.tmpchi, 'w') as f:
f.write('\n'.join([str(val) for val in self.lchi]))
index = self.la.index(word)
- parametres = {'type' : 'clustersimitxt',
+ parametres = {'type' : 'clustersimitxt',
'pathout' : self.Source.parametres['pathout'],
'word' : index ,
'lem' : self.Source.parametres['lem'],
self.tmpchi = os.path.join(self.Source.parametres['pathout'],'chi_%i.csv' % self.cl)
with open(self.tmpchi, 'w') as f:
f.write('\n'.join([str(val) for val in self.lchi]))
- parametres = {'type' : 'clustersimitxt',
+ parametres = {'type' : 'clustersimitxt',
'pathout' : self.Source.parametres['pathout'],
'lem' : self.Source.parametres['lem'],
'tmpchi' : self.tmpchi}
#win.html = '<html>\n' + '<br>'.join(['<br>'.join([ucis_txt[i], '<table bgcolor = #1BF0F7 border=0><tr><td><b>score : %.2f</b></td></tr></table>' % ntab2[i][0], ucestxt[i]]) for i in range(0,len(ucestxt))]) + '\n</html>'
#win.HtmlPage.SetPage(win.html)
win.Show(True)
-
+
def on_tablex(self, evt):
if 'corpus' in dir(self.Source):
corpus = self.Source.corpus
ListWord.append(self.getColumnText(last, 6))
ucef = []
if self.Source.parametres['classif_mode'] != 2 :
- for word in ListWord :
+ for word in ListWord :
uci = False
ucef += list(set(corpus.getlemuces(word)).intersection(uces))
else :
- for word in ListWord :
- ucef += list(set(corpus.getlemucis(word)).intersection(uces))
+ for word in ListWord :
+ ucef += list(set(corpus.getlemucis(word)).intersection(uces))
uci = True
ucis_txt, ucestxt = doconcorde(corpus, ucef, ListWord, uci = uci)
items = dict([[i, '<br><br>'.join([ucis_txt[i], ucestxt[i]])] for i in range(0,len(ucestxt))])
uces = corpus.lc[self.cl-1]
win = self.make_concord(uces, ' - '.join([_(u"Concordance").decode('utf8'), "Classe %i" % self.cl]))
win.Show(True)
-
+
def OnPopupThree(self, event):
corpus = self.Source.corpus
uces = [classe[i] for classe in corpus.lc for i in range(0,len(classe))]
win = self.make_concord(uces, ' - '.join([_(u"Concordance").decode('utf8'), _(u"Segments of this clustering").decode('utf8')]))
win.Show(True)
-
+
def OnPopupFour(self, event):
corpus = self.Source.corpus
uces = [classe[i] for classe in corpus.lc for i in range(0,len(classe))] + corpus.lc0
lk = "http://www.cnrtl.fr/definition/" + word
webbrowser.open(lk)
- def OnPopupSix(self, event):
+ def OnPopupSix(self, event):
word = self.getColumnText(self.GetFirstSelected(), 6)
lk = "http://www.cnrtl.fr/etymologie/" + word
webbrowser.open(lk)
-
- def OnPopupSeven(self, event):
+
+ def OnPopupSeven(self, event):
word = self.getColumnText(self.GetFirstSelected(), 6)
lk = "http://www.cnrtl.fr/synonymie/" + word
webbrowser.open(lk)
-
- def OnPopupHeight(self, event):
+
+ def OnPopupHeight(self, event):
word = self.getColumnText(self.GetFirstSelected(), 6)
lk = "http://www.cnrtl.fr/antonymie/" + word
webbrowser.open(lk)
-
- def OnPopupNine(self, event):
+
+ def OnPopupNine(self, event):
word = self.getColumnText(self.GetFirstSelected(), 6)
lk = "http://www.cnrtl.fr/morphologie/" + word
webbrowser.open(lk)
#win.html = '<html>\n' + '<br>'.join([' : '.join([str(val) for val in forme]) for forme in rep]) + '\n</html>'
#win.HtmlPage.SetPage(win.html)
win.Show(True)
-
+
def OnMakeTgen(self, evt):
- self.parent.tree.OnTgenEditor(self.getselectedwords())
+ self.parent.tree.OnTgenEditor(self.getselectedwords())
class wliste(wx.Frame):
self.SetAutoLayout(True)
self.SetSizer(sizer_1)
self.Layout()
-
+
def OnCloseMe(self, event):
self.Close(True)
--- /dev/null
+
+
+load('mariagepourtousnov-jui_corpus_corpus_1/mariagepourtousnov-jui_corpus_alceste_2/RData.RData')
+load('mariagegaynov-jui_corpus_corpus_1/mariagegaynov-jui_corpus_alceste_3/RData.RData')
+load('mariagehomonov-jui_corpus_corpus_1/mariagehomonov-jui_corpus_alceste_2/RData.RData')
+
+dpt <- chistabletot[tc,]
+#dpt <- chistabletot[debet:nrow(chistabletot),]
+dd <-rownames(dpt)
+dd <- strptime(dd, "*date_%Y-%m-%d")
+dd <- strptime(dd, "%Y-%m-%d")
+dd <- cbind(as.character(dd), dpt)
+dd <- dd[order(dd[,1]),]
+dd <- add.missing.date(dd,c.dates = 1, datedeb=c(07,11,2012), datefin=c(31,07,2013))
+
+#tot <- afctable[debet:nrow(afctable),]
+tot <- afctable[tc,]
+tt <- rownames(tot)
+tt <- strptime(tt, "*date_%Y-%m-%d")
+tt <- strptime(tt, "%Y-%m-%d")
+tt <- cbind(as.character(tt), tot)
+tt <- tt[order(tt[,1]),]
+tt <- add.missing.date(tt, c.dates = 1, datedeb=c(07,11,2012), datefin=c(31,07,2013))
+
+rn <- tt[,1]
+tt <- tt[,-1]
+tt <- apply(tt, 2, as.numeric)
+rownames(tt) <- rn
+tcp <- rowSums(tt)
+ptc <- tcp/sum(tcp)
+
+ptt <- prop.table(as.matrix(tt), 1)
+
+tcl <- table(classes)
+z <- which(names(tcl)=="0")
+if (length(z) != 0) {tcl <- tcl[-z]}
+tclp <- tcl/sum(tcl)
+
+
+
+rn <- dd[,1]
+dd <- dd[,-1]
+dd <- apply(dd,2, as.numeric)
+rownames(dd) <- rn
+
+
+
+library(ape)
+
+
+tree1 <- tree.cut1$tree.cl
+tree1 <- compute.brlen(tree1)
+tree1 <- as.hclust(tree1)
+
+
+
+dd <- t(dd)
+
+cc <- dd
+cc[which(dd <= (-3.84))] <- 1
+cc[which((dd > (-3.84)) & (dd < 3.84))] <- 2
+cc[which(dd >= 3.84)] <- 3
+library(RColorBrewer)
+#col <- brewer.pal(3, 'Reds')
+#col <- c('red', 'green', 'blue')
+col <- c('black', 'black', 'red')
+col <- c('white', 'white', 'blue')
+col <- col[cc]
+
+
+clod <- rev(as.numeric(tree.cut1$tree.cl$tip.label))
+
+heatmap(as.matrix(dd[as.numeric(tree.cut1$tree.cl$tip.label),]), Colv=NA, Rowv=as.dendrogram(tree1), col=col)
+
+png('cl_dates_homo.png', h=1000, w=2500)
+alphas <- seq(0,1, length.out=length(breaks))
+#par(mfrow=c(nrow(dd),1))
+par(mar=c(3,3,3,3))
+layout(matrix(c(rep(1,nrow(dd)),c(2:(nrow(dd)+1)),c(rep(nrow(dd)+2, nrow(dd)))),ncol=3), heights=tclp[clod], widths=c(0.05,0.92,0.03))
+par(mar=c(0,0,0,0))
+plot.phylo(tree.cut1$tree.cl,label.offset=0.1)
+for (i in clod) {
+ print(i)
+ par(mar=c(0,0,0,0))
+ lcol <- cut(dd[i,], breaks, include.lowest=TRUE)
+ ulcol <- names(table(lcol))
+ lcol <- as.character(lcol)
+ for (j in 1:length(ulcol)) {
+ lcol[which(lcol==ulcol[j])] <- j
+ }
+ lcol <- as.numeric(lcol)
+
+ #lcol[which(lcol <= 9)] <- 1
+
+ mcol <- rainbow(nrow(dd))[i]
+ last.col <- NULL
+ for (k in alphas) {
+ last.col <- c(last.col, rgb(r=col2rgb(mcol)[1]/255, g=col2rgb(mcol)[2]/255, b=col2rgb(mcol)[3]/255, a=k))
+ }
+ print(last.col)
+
+ barplot(rep(1,ncol(dd)), width=ptc, names.arg=FALSE, axes=FALSE, col=last.col[lcol], border=rgb(r=0, g=0, b=0, a=0.3))
+#val2col(dd[i,], col=heat.colors(30)), border=NA)
+}
+plot.new()
+legend('right', as.character(lk), fill=last.col)
+
+dev.off()
+
+
+layout(matrix(c(rep(1,nrow(dd)),c(2:(nrow(dd)+1)),c(rep(nrow(dd)+2, nrow(dd)))),ncol=3), heights=tclp[clod], widths=c(0.05,0.92,0.03))
+par(mar=c(0,0,0,0))
+plot.phylo(tree.cut1$tree.cl,label.offset=0.1)
+ncol <- rainbow(nrow(dd))
+for (i in clod) {
+ print(i)
+ par(mar=c(0,0,0,0))
+ barplot(dd[i,], width=ptc, names.arg=FALSE, axes=FALSE, col=ncol[i])
+}
+
+
+
+
+vcol <- rainbow(nrow(dd))
+ncoli <- dd
+for (i in 1:nrow(dd)) {
+ lcol <- cut(dd[1,], breaks, include.lowest=TRUE)
+ ulcol <- names(table(lcol))
+ lcol <- as.character(lcol)
+ rlcol <- rank()
+ for (i in 1:length(ulcol)) {
+ lcol[which(lcol==ulcol[i])] <- i
+ }
+ lcol <- as.numeric(lcol)
+ for (j in 1:ncol(dd)) {
+ if (dd[i,j] < 3.84) {
+ ncoli[i,j] <- rgb(r=col2rgb(vcol[i])[1]/255, g=col2rgb(vcol[i])[2]/255, b=col2rgb(vcol[i])[3]/255, a=0.2)
+ } else {
+ ncoli[i,j] <- rgb(r=col2rgb(vcol[i])[1]/255, g=col2rgb(vcol[i])[2]/255, b=col2rgb(vcol[i])[3]/255, a=1)
+ }
+ }
+}
+
+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)
+
+layout(matrix(c(1:nrow(ptt)), nrow=1), widths=ptc)
+od <- as.numeric(tree.cut1$tree.cl$tip.label)
+colod = rainbow(ncol(ptt))[od]
+for (i in 1:ncol(ptt)) {
+ par(mar=c(0,0,0,0))
+ barplot(as.matrix(ptt[i,od], ncol=1), col=colod, axes=FALSE)
+}
+
+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)
+#lcol <- c(-rev(lcol), lcol)
+#lk <- c(-rev(lk), lk)
+#lcol <- c(min(dd), lcol)
+#lk <- c(1, lk)
+#breaks <- c(lcol, max(dd))
+breaks <- lcol
+
+lcol <- cut(dd[1,], breaks)
+ulcol <- names(table(lcol))
+lcol <- as.character(lcol)
+for (i in 1:length(ulcol)) {
+ lcol[which(lcol==ulcol[i])] <- i
+}
+lcol <- as.numeric(lcol)
+
+
+make.chi <- function(x) {
+ rs <- rowSums(x)
+ cs <- colSums(x)
+ n <- sum(x)
+
+}
+
+
+
+select.chi.classe <- function(tablechi, nb, active = TRUE) {
+ rowkeep <- NULL
+ if (active & !is.null(debsup)) {
+ print(debsup)
+ print('###############################################################@')
+ tablechi <- tablechi[1:(debsup-1),]
+ } else if (!active & !is.null(debsup)) {
+ tablechi <- tablechi[debsup:(debet-1),]
+ }
+ if (nb > nrow(tablechi)) {
+ nb <- nrow(tablechi)
+ }
+ for (i in 1:ncol(tablechi)) {
+ rowkeep <- append(rowkeep,order(tablechi[,i], decreasing = TRUE)[1:nb])
+ }
+ rowkeep <- unique(rowkeep)
+ rowkeep
+}
+
+
+plot.dendro.cloud <- function(tree, classes, chisqtable, nbbycl = 60, type.dendro = "phylogram", max.cex=2, min.cex=0.3, from.cmd = FALSE, bw = FALSE, lab = NULL, do.cloud=FALSE) {
+ library(wordcloud)
+ library(ape)
+ classes<-classes[classes!=0]
+ classes<-as.factor(classes)
+ sum.cl<-as.matrix(summary(classes, maxsum=1000000))
+ sum.cl<-(sum.cl/colSums(sum.cl)*100)
+ sum.cl<-round(sum.cl,2)
+ sum.cl<-cbind(sum.cl,as.matrix(100-sum.cl[,1]))
+ sum.cl <- sum.cl[,1]
+ tree.order<- as.numeric(tree$tip.label)
+ vec.mat<-NULL
+
+ for (i in 1:length(sum.cl)) vec.mat<-append(vec.mat,1)
+ v<-2
+ for (i in 1:length(sum.cl)) {
+ vec.mat<-append(vec.mat,v)
+ v<-v+1
+ }
+ if (!do.cloud) {
+ layout(matrix(vec.mat,length(sum.cl),2), heights=tclp[clod], widths=c(0.15,0.85))
+ } else {
+ row.keep <- select.chi.classe(chisqtable, nbbycl)
+ toplot <- chisqtable[row.keep,]
+ lclasses <- list()
+ for (classe in 1:length(sum.cl)) {
+ ntoplot <- toplot[,classe]
+ ntoplot <- ntoplot[order(ntoplot, decreasing = TRUE)]
+ ntoplot <- round(ntoplot, 0)
+ ntoplot <- ntoplot[1:nbbycl]
+ ntoplot <- ntoplot[order(ntoplot)]
+ #ntoplot <- ifelse(length(ntoplot) > nbbycl, ntoplot[1:nbbycl], ntoplot)
+ lclasses[[classe]] <- ntoplot
+ }
+ sup.keep <- select.chi.classe(chisqtable, nbbycl, active = FALSE)
+ toplot.sup <- chisqtable[debsup:(debet+1),]
+ toplot.sup <- toplot.sup[sup.keep, ]
+ lsup <- list()
+ for (classe in 1:length(sum.cl)) {
+ ntoplot <- toplot.sup[,classe]
+ ntoplot <- ntoplot[order(ntoplot, decreasing = TRUE)]
+ ntoplot <- round(ntoplot, 0)
+ ntoplot <- ntoplot[1:nbbycl]
+ ntoplot <- ntoplot[order(ntoplot)]
+ #ntoplot <- ifelse(length(ntoplot) > nbbycl, ntoplot[1:nbbycl], ntoplot)
+ lsup[[classe]] <- ntoplot
+ }
+ layout(matrix(c(rep(1,nrow(dd)),c(2:(nrow(dd)+1)),c((nrow(dd)+2):(2*nrow(dd)+1)), c((2*nrow(dd)+2):(3*nrow(dd)+1))),ncol=4), heights=tclp[clod], widths=c(0.05,0.05,0.05, 0.85))
+ }
+
+ if (! bw) {
+ col <- rainbow(length(sum.cl))[as.numeric(tree$tip.label)]
+ colcloud <- rainbow(length(sum.cl))
+ }
+ par(mar=c(0,0,0,0))
+ label.ori<-tree[[2]]
+ if (!is.null(lab)) {
+ tree$tip.label <- lab
+ } else {
+ tree[[2]]<-paste('classe ',tree[[2]])
+ }
+ plot.phylo(tree,label.offset=0.1,tip.col=col, type=type.dendro)
+ if (do.cloud) {
+ for (i in rev(tree.order)) {
+ par(mar=c(0,0,1,0),cex=0.9)
+ wordcloud(names(lclasses[[i]]), lclasses[[i]], scale = c(max.cex, min.cex), random.order=FALSE, colors = colcloud[i])
+ }
+ for (i in rev(tree.order)) {
+ par(mar=c(0,0,1,0),cex=0.9)
+ wordcloud(names(lsup[[i]]), lsup[[i]], scale = c(max.cex, min.cex), random.order=FALSE, colors = colcloud[i])
+ }
+ }
+
+ for (i in rev(tree.order)) {
+ par(mar=c(0,0,0,0))
+ lcol <- cut(dd[i,], breaks, include.lowest=TRUE)
+ ulcol <- names(table(lcol))
+ lcol <- as.character(lcol)
+ for (j in 1:length(ulcol)) {
+ lcol[which(lcol==ulcol[j])] <- j
+ }
+ lcol <- as.numeric(lcol)
+
+ #lcol[which(lcol <= 9)] <- 1
+
+ mcol <- rainbow(nrow(dd))[i]
+ last.col <- NULL
+ for (k in alphas) {
+ last.col <- c(last.col, rgb(r=col2rgb(mcol)[1]/255, g=col2rgb(mcol)[2]/255, b=col2rgb(mcol)[3]/255, a=k))
+ }
+ print(last.col)
+
+ barplot(rep(1,ncol(dd)), width=ptc, names.arg=FALSE, axes=FALSE, col=last.col[lcol], border=rgb(r=0, g=0, b=0, a=0.3))
+
+ }
+}
+
+
+filename.to.svg <- function(filename) {
+ filename <- gsub('.png', '.svg', filename)
+ return(filename)
+}
+
+open_file_graph <- function (filename, width=800, height = 800, quality = 100, svg = FALSE) {
+ if (Sys.info()["sysname"] == 'Darwin') {
+ width <- width/74.97
+ height <- height/74.97
+ if (!svg) {
+ quartz(file = filename, type = 'png', width = width, height = height)
+ } else {
+ svg(filename.to.svg(filename), width=width, height=height)
+ }
+ } else {
+ if (svg) {
+ svg(filename.to.svg(filename), width=width/74.97, height=height/74.97)
+ } else {
+ png(filename, width=width, height=height)#, quality = quality)
+ }
+ }
+}
+
+
+
+open_file_graph('cl_cloud_dates_gay.png', height=900, width=2500, svg=TRUE)
+plot.dendro.cloud(tree.cut1$tree.cl, classes, chistabletot, from.cmd=TRUE)
+
+dev.off()
projects / iramuteq / commitdiff