R/scattermap.R

In GeoXp: Interactive exploratory spatial data analysis

`scattermap` <- function(sp.obj, names.var, lin.reg=TRUE, quantiles=TRUE,
names.attr=names(sp.obj), criteria=NULL, carte=NULL, identify=FALSE, cex.lab=0.8,
pch=16, col="lightblue3",xlab="", ylab="", axes=FALSE, lablong="", lablat="")
{
envir = as.environment(1)
# Verification of the Spatial Object sp.obj
class.obj<-class(sp.obj)[1]
spdf<-(class.obj=="SpatialPolygonsDataFrame")
if(substr(class.obj,1,7)!="Spatial") stop("sp.obj may be a Spatial object")
if(substr(class.obj,nchar(class.obj)-8,nchar(class.obj))!="DataFrame") stop("sp.obj should contain a data.frame")
if(!is.numeric(names.var) & length(match(names.var,names(sp.obj)))!=length(names.var) ) stop("At least one component of names.var is not included in the data.frame of sp.obj")
if(length(names.attr)!=length(names(sp.obj))) stop("names.attr should be a vector of character with a length equal to the number of variable")


# we propose to refind the same arguments used in first version of GeoXp
long<-coordinates(sp.obj)[,1]
lat<-coordinates(sp.obj)[,2]

var1<-sp.obj@data[,names.var[1]]
var2<-sp.obj@data[,names.var[2]]

listvar<-sp.obj@data
listnomvar<-names.attr


# Code which was necessary in the previous version
# if(is.null(carte) & class.obj=="SpatialPolygonsDataFrame") carte<-spdf2list(sp.obj)$poly

 # for identifyng the selected sites
ifelse(identify, label<-row.names(listvar),label<-"")

# initialisation
nointer<-FALSE
nocart<-FALSE
buble<-FALSE
maptt<-FALSE
z<-NULL
legmap<-NULL
legends<-list(FALSE,FALSE,"","")
labvar=c(xlab,ylab)
obs<-vector(mode = "logical", length = length(long))

var1=as.matrix(var1)
var2=as.matrix(var2)
lat=as.matrix(lat)
long=as.matrix(long)

graphChoice <- ""
varChoice1 <- ""
varChoice2 <- ""
choix <- ""
listgraph <- c("Histogram","Barplot","Scatterplot")

labmod <- ""
col2 <- "blue"
col3 <- col[1]
method <- ""
pch2 <- pch[1]

# transformation data.frame en matrix
if((length(listvar)>0)&&(dim(as.matrix(listvar))[2]==1)) listvar<-as.matrix(listvar)

# Windows device
if(!(2%in%dev.list())) dev.new()
if(!(3%in%dev.list())) dev.new()


# au sujet des quantiles conditionnels    
#if (lin.reg || length(quantiles)!=0)
#{
#    u1 <- sort(var1)
#    u1 <- as.vector(u1)
#    z <- seq(min(u1), max(u1), by = ((max(u1)-min(u1))/1000))
#    z <- round(z)
#    z1 <- z[2:length(z)] - z[1:(length(z) - 1)]
#    h <- mean(z1)
#
#    p <- 1 / (1 + (h^3 / 6))
#    p1 <- 1 / (1 + (h^3 / 1000)) #60
#    p2 <- 1 / (1 + (h^3 / 4)) #0.6
#    alpha <- (1 - p) / p
#    borne1 <- (1 - p1) / p1
#    borne2 <- (1 - p2) / p2
#
#}


borne1=0.01
borne2=0.99
alpha=0.5

names.slide=c("Value of alpha-quantile")

####################################################
# sélection d'un point
####################################################

pointfunc<-function() 
{
    quit <- FALSE;

     if(maptt) 
      { dev.set(2)
        title("ACTIVE DEVICE", cex.main = 0.8, font.main = 3, col.main='red')
        title(sub = "To stop selection, click on the right button of the mouse and stop (for MAC, ESC)", cex.sub = 0.8, font.sub = 3,col.sub='red')
         if(spdf & nrow(sp.obj)>85 & !buble) 
         {points(long,lat,pch=16,col='royalblue')}
      }
     else
     { dev.set(3)
       title("ACTIVE DEVICE", cex.main = 0.8, font.main = 3, col.main='red')
       title(sub = "To stop selection, click on the right button of the mouse and stop (for MAC, ESC)", cex.sub = 0.8, font.sub = 3,col.sub='red')
     }
     
    while(!quit)
    {
        if(maptt) 
        {
           dev.set(2)
           if(spdf & nrow(sp.obj)>75 & !buble) 
            {points(long,lat,pch=16,col='royalblue')}
            loc<-locator(1)
            if(is.null(loc)) 
            {
              quit<-TRUE
              carte(long=long, lat=lat,obs=obs, sp.obj=sp.obj, buble=buble,cbuble=z,criteria=criteria,nointer=nointer,  label=label,
              symbol=pch2, couleurs=col2,carte=carte,nocart=nocart,legmap=legmap,legends=legends,axis=axes, labmod=labmod,
              lablong=lablong,lablat=lablat,cex.lab=cex.lab,method=method,classe=listvar[,which(listnomvar == varChoice1)]) 
              next
            }           
           if(!spdf|nrow(sp.obj)>75)
          {obs<<-selectmap(var1=long,var2=lat,obs=obs,Xpoly=loc[1], Ypoly=loc[2], method="point")}
           else
          {if(gContains(sp.obj,SpatialPoints(cbind(loc$x,loc$y),proj4string=CRS(proj4string(sp.obj)))))
           {for (i in 1:nrow(sp.obj))
            {if(gContains(sp.obj[i,],SpatialPoints(cbind(loc$x,loc$y),proj4string=CRS(proj4string(sp.obj)))))
             {obs[i]<<-!obs[i]
              break
              }  
            }
           } 
          }
        }
        else
        {
            dev.set(3)
            loc<-locator(1)
            if(is.null(loc)) 
            {
              quit<-TRUE
              graphique(var1=var1, var2=var2, obs=obs, num=3, graph="Scatterplot", labvar=labvar, symbol=pch, couleurs=col,
              opt1=lin.reg, quantiles=quantiles, alpha1=alpha)
              next
            }
            obs<<-selectmap(var1=var1,var2=var2,obs=obs,Xpoly=loc[1], Ypoly=loc[2], method="point")
        }
        
        #graphiques     
      graphique(var1=var1, var2=var2, obs=obs, num=3, graph="Scatterplot", labvar=labvar, symbol=pch, couleurs=col,
      opt1=lin.reg, quantiles=quantiles, alpha1=alpha)
      
      carte(long=long, lat=lat,obs=obs, sp.obj=sp.obj, buble=buble,cbuble=z,criteria=criteria,nointer=nointer,  label=label,
      symbol=pch2, couleurs=col2,carte=carte,nocart=nocart,legmap=legmap,legends=legends,axis=axes, labmod=labmod,
      lablong=lablong,lablat=lablat,cex.lab=cex.lab,method=method,classe=listvar[,which(listnomvar == varChoice1)]) 
  
     if(maptt) 
      { dev.set(2)
        title("ACTIVE DEVICE", cex.main = 0.8, font.main = 3, col.main='red')
        title(sub = "To stop selection, click on the right button of the mouse and stop (for MAC, ESC)", cex.sub = 0.8, font.sub = 3,col.sub='red')
      }
     else
     { dev.set(3)
       title("ACTIVE DEVICE", cex.main = 0.8, font.main = 3, col.main='red')
       title(sub = "To stop selection, click on the right button of the mouse and stop (for MAC, ESC)", cex.sub = 0.8, font.sub = 3,col.sub='red')
     }
     
        if ((graphChoice != "") && (varChoice1 != "") && (length(dev.list()) > 2))
        {
            graphique(var1=listvar[,which(listnomvar == varChoice1)], var2=listvar[,which(listnomvar == varChoice2)],
            obs=obs, num=4, graph=graphChoice, couleurs=col3,symbol=pch, labvar=c(varChoice1,varChoice2))
        }

    }
  }

####################################################
# sélection d'un point sur la carte
####################################################

pt1func <- function()
{   maptt <<- TRUE
    pointfunc()
  }

####################################################
# sélection d'un point sur le graphique
####################################################

pt2func <- function()
{
    maptt <<- FALSE
    pointfunc()
  }

####################################################
# sélection d'un polygone
####################################################

polyfunc<-function() 
{
    polyX <- NULL
    polyY <- NULL
    quit <- FALSE

     if(maptt) 
      { dev.set(2)
        title("ACTIVE DEVICE", cex.main = 0.8, font.main = 3, col.main='red')
        title(sub = "To stop selection, click on the right button of the mouse and stop (for MAC, ESC)", cex.sub = 0.8, font.sub = 3,col.sub='red')
        if(spdf) {points(long,lat,pch=16,col='royalblue')}
      }
     else
     { dev.set(3)
       title("ACTIVE DEVICE", cex.main = 0.8, font.main = 3, col.main='red')
       title(sub = "To stop selection, click on the right button of the mouse and stop (for MAC, ESC)", cex.sub = 0.8, font.sub = 3,col.sub='red')
     }
     
    while(!quit)
    {
        if(maptt)
        {
            dev.set(2)
            loc<-locator(1)
            if(is.null(loc)) 
            {
                quit<-TRUE
                next
            }
        }
        else
        {
            dev.set(3)
            loc<-locator(1)
            if(is.null(loc)) 
            {
                quit<-TRUE
                next
            }   
        }
        polyX <- c(polyX, loc[1])
        polyY <- c(polyY, loc[2])
        lines(polyX,polyY);
    }
    polyX <- c(polyX, polyX[1])
    polyY <- c(polyY, polyY[1])
 
 if (length(polyX)>0)
 {
    lines(polyX,polyY)

    if (maptt)
    {
        obs <<- selectmap(var1=long, var2=lat, obs=obs, Xpoly=polyX, Ypoly=polyY, method="poly");
    }
    else
    {
        obs <<- selectmap(var1=var1, var2=var2, obs=obs, Xpoly=polyX, Ypoly=polyY, method="poly");
    }

    #graphiques
      graphique(var1=var1, var2=var2, obs=obs, num=3, graph="Scatterplot", labvar=labvar, symbol=pch, couleurs=col,
      opt1=lin.reg, quantiles=quantiles, alpha1=alpha)
      
      carte(long=long, lat=lat,obs=obs, sp.obj=sp.obj, buble=buble,cbuble=z,criteria=criteria,nointer=nointer,  label=label,
      symbol=pch2, couleurs=col2,carte=carte,nocart=nocart,legmap=legmap,legends=legends,axis=axes, labmod=labmod,
      lablong=lablong,lablat=lablat,cex.lab=cex.lab,method=method,classe=listvar[,which(listnomvar == varChoice1)]) 
  
        if ((graphChoice != "") && (varChoice1 != "") && (length(dev.list()) > 2))
        {
            graphique(var1=listvar[,which(listnomvar == varChoice1)], var2=listvar[,which(listnomvar == varChoice2)],
            obs=obs, num=4, graph=graphChoice, couleurs=col3,symbol=pch, labvar=c(varChoice1,varChoice2))
        }
 }
}

####################################################
# sélection d'un polygone sur la carte
####################################################

poly1func <- function()
{
   # SGfunc()
    maptt <<- TRUE
   polyfunc()
  }

####################################################
# sélection d'un polygone sur le graphique
####################################################

poly2func <- function()
{
   # SGfunc()
    maptt <<- FALSE
    polyfunc()
  }

####################################################
# contour des unités spatiales
####################################################
cartfunc <- function()
{  
 if (length(carte) != 0)
   {
    ifelse(!nocart,nocart<<-TRUE,nocart<<-FALSE)
    carte(long=long, lat=lat,obs=obs, sp.obj=sp.obj, buble=buble,cbuble=z,criteria=criteria,nointer=nointer,  label=label,
    symbol=pch2, couleurs=col2,carte=carte,nocart=nocart,legmap=legmap,legends=legends,axis=axes, labmod=labmod,
    lablong=lablong,lablat=lablat,cex.lab=cex.lab,method=method,classe=listvar[,which(listnomvar == varChoice1)]) 
   }
   else
   {
    tkmessageBox(message="Spatial contours have not been given",icon="warning",type="ok")    
   }
}


####################################################
# choix d'un autre graphique
####################################################

graphfunc <- function()
{ 
   if ((length(listvar) != 0) && (length(listnomvar) != 0))
    {
        choix <<- selectgraph(listnomvar,listgraph)
        varChoice1 <<- choix$varChoice1
        varChoice2 <<- choix$varChoice2
        graphChoice <<- choix$graphChoice
           
        if ((graphChoice != "") && (varChoice1 != ""))
        {
          if (((graphChoice == "Histogram")&&(!is.numeric(listvar[,which(listnomvar == varChoice1)])))||((graphChoice == "Scatterplot")&&((!is.numeric(listvar[,which(listnomvar == varChoice1)]))||(!is.numeric(listvar[,which(listnomvar == varChoice2)]))))) 
           {
            tkmessageBox(message="Variables choosed are not in a good format",icon="warning",type="ok")
           }
          else
           {
            res1<-choix.couleur(graphChoice,listvar,listnomvar,varChoice1,legends,col,pch,spdf=spdf)
            
            method <<- res1$method
            col2 <<- res1$col2
            col3 <<- res1$col3
            pch2 <<- res1$pch2
            legends <<- res1$legends
            labmod <<- res1$labmod
                     
            if(!(4%in%dev.list())) dev.new()
            graphique(var1=listvar[,which(listnomvar == varChoice1)], var2=listvar[,which(listnomvar == varChoice2)],
            obs=obs, num=4, graph=graphChoice, couleurs=col3,symbol=pch, labvar=c(varChoice1,varChoice2))    
            
            carte(long=long, lat=lat,obs=obs, sp.obj=sp.obj, buble=buble,cbuble=z,criteria=criteria,nointer=nointer,  label=label,
            symbol=pch2, couleurs=col2,carte=carte,nocart=nocart,legmap=legmap,legends=legends,axis=axes, labmod=labmod,
            lablong=lablong,lablat=lablat,cex.lab=cex.lab,method=method,classe=listvar[,which(listnomvar == varChoice1)]) 
           }
       }   
   }
   else
   {
    tkmessageBox(message="Variables (listvar) and their names (listnomvar) must have been given",icon="warning",type="ok")
   }  
}

####################################################
# rafraichissement des graphiques
####################################################

SGfunc<-function() 
{
 obs<<-vector(mode = "logical", length = length(long));

 # graphiques
  graphique(var1=var1, var2=var2, obs=obs, num=3, graph="Scatterplot", labvar=labvar, symbol=pch, couleurs=col,
  opt1=lin.reg, quantiles=quantiles, alpha1=alpha)
      
  carte(long=long, lat=lat,obs=obs, sp.obj=sp.obj, buble=buble,cbuble=z,criteria=criteria,nointer=nointer,  label=label,
  symbol=pch2, couleurs=col2,carte=carte,nocart=nocart,legmap=legmap,legends=legends,axis=axes, labmod=labmod,
  lablong=lablong,lablat=lablat,cex.lab=cex.lab,method=method,classe=listvar[,which(listnomvar == varChoice1)]) 
 
   if ((graphChoice != "") && (varChoice1 != "") && (length(dev.list()) > 2))
    {
     graphique(var1=listvar[,which(listnomvar == varChoice1)], var2=listvar[,which(listnomvar == varChoice2)],
     obs=obs, num=4, graph=graphChoice, couleurs=col3,symbol=pch, labvar=c(varChoice1,varChoice2))
    } 
}

####################################################
# quitter l'application
####################################################

quitfunc<-function()
{
    #tclvalue(fin)<<-TRUE
    tkdestroy(tt)
    assign("GeoXp.open", FALSE, envir = baseenv())
    dev.set(3)
    layout(1)
    par(mar=c(5.1,4.1,4.1,2.1))
   # assign("obs", row.names(sp.obj)[obs], envir = .GlobalEnv)
}

quitfunc2<-function()
{
    #tclvalue(fin)<<-TRUE
    tkdestroy(tt)
    assign("GeoXp.open", FALSE, envir = baseenv())
    dev.set(3)
    layout(1)
    par(mar=c(5.1,4.1,4.1,2.1))
    print("Results have been saved in last.select object")
    assign("last.select", which(obs), envir = envir)
}

####################################################
# modification du alpha de l'estimateur
####################################################
  
refresh.code<-function(...)
{
  alpha<<-slider1(names.slide=names.slide,no=1)
  graphique(var1=var1, var2=var2, obs=obs, num=3, graph="Scatterplot", labvar=labvar, symbol=pch, couleurs=col,
  opt1=lin.reg, quantiles=quantiles, alpha1=alpha)
  }


####################################################
# Open a no interactive selection
####################################################

fnointer<-function() 
{
 if (length(criteria) != 0)
 {
  ifelse(!nointer,nointer<<-TRUE,nointer<<-FALSE)
  carte(long=long, lat=lat, obs=obs, sp.obj=sp.obj, buble=buble,cbuble=z,criteria=criteria,nointer=nointer,  label=label,
  symbol=pch2, couleurs=col2,carte=carte,nocart=nocart,legmap=legmap,legends=legends,axis=axes, labmod=labmod,
  lablong=lablong,lablat=lablat,cex.lab=cex.lab,method=method,classe=listvar[,which(listnomvar == varChoice1)]) 
 }
 else
 {
  tkmessageBox(message="Criteria has not been given",icon="warning",type="ok")
 }
 
}
####################################################
# Bubble
####################################################

fbubble<-function()
{
  res2<-choix.bubble(buble,listvar,listnomvar,legends)
  
  buble <<- res2$buble
  legends <<- res2$legends
  z <<- res2$z
  legmap <<- res2$legmap
  
  carte(long=long, lat=lat,obs=obs, sp.obj=sp.obj, buble=buble,cbuble=z,criteria=criteria,nointer=nointer,  label=label,
  symbol=pch2, couleurs=col2,carte=carte,nocart=nocart,legmap=legmap,legends=legends,axis=axes, labmod=labmod,
  lablong=lablong,lablat=lablat,cex.lab=cex.lab,method=method,classe=listvar[,which(listnomvar == varChoice1)]) 

}

####################################################
# Représentation des graphiques
####################################################
# Is there a Tk window already open ?
if(interactive())
{
 if(!exists("GeoXp.open",envir = baseenv())||length(ls(envir=.TkRoot$env, all.names=TRUE))==2)
 {
  graphique(var1=var1, var2=var2, obs=obs, num=3, graph="Scatterplot", labvar=labvar, symbol=pch, couleurs=col,
  opt1=lin.reg, quantiles=quantiles, alpha1=alpha)
      
  carte(long=long, lat=lat,obs=obs, sp.obj=sp.obj, buble=buble,cbuble=z,criteria=criteria,nointer=nointer,  label=label,
  symbol=pch2, couleurs=col2,carte=carte,nocart=nocart,legmap=legmap,legends=legends,axis=axes, labmod=labmod,
  lablong=lablong,lablat=lablat,cex.lab=cex.lab,method=method,classe=listvar[,which(listnomvar == varChoice1)]) 
  assign("GeoXp.open", TRUE, envir = baseenv())
 }
 else
 {if(get("GeoXp.open",envir= baseenv()))
   {stop("Warning : a GeoXp function is already open. Please, close Tk window before calling a new GeoXp function to avoid conflict between graphics")}
  else
  {graphique(var1=var1, var2=var2, obs=obs, num=3, graph="Scatterplot", labvar=labvar, symbol=pch, couleurs=col,
   opt1=lin.reg, quantiles=quantiles, alpha1=alpha)
      
  carte(long=long, lat=lat,obs=obs, sp.obj=sp.obj, buble=buble,cbuble=z,criteria=criteria,nointer=nointer,  label=label,
   symbol=pch2, couleurs=col2,carte=carte,nocart=nocart,legmap=legmap,legends=legends,axis=axes, labmod=labmod,
   lablong=lablong,lablat=lablat,cex.lab=cex.lab,method=method,classe=listvar[,which(listnomvar == varChoice1)]) 
   assign("GeoXp.open", TRUE, envir = baseenv())}
 }
}



####################################################
# création de la boite de dialogue
####################################################
if(interactive())
{
fontheading<-tkfont.create(family="times",size=14,weight="bold")

tt <- tktoplevel()
tkwm.title(tt, "scattermap")

frame1a <- tkframe(tt, relief = "groove", borderwidth = 2, background = "white")
tkpack(tklabel(frame1a, text = "Interactive selection", font = "Times 14",
foreground = "blue", background = "white"))
tkpack(tklabel(frame1a, text = "Work on the map", font = "Times 12",
foreground = "darkred", background = "white"))
point.but <- tkbutton(frame1a, text="Selection by point", command=pt1func);
poly.but <- tkbutton(frame1a, text="Selection by polygon ", command=poly1func);
tkpack(point.but, poly.but, side = "left", expand = "TRUE",fill = "x")
tkpack(frame1a, expand = "TRUE", fill = "x")

frame1c <- tkframe(tt, relief = "groove", borderwidth = 2, background = "white")
tkpack(tklabel(frame1c, text = "Work on the graphic", font = "Times 12",
foreground = "darkred", background = "white"))
point.but2 <- tkbutton(frame1c, text="Selection by point", command=pt2func);
poly.but2 <- tkbutton(frame1c, text="Selection by polygon ", command=poly2func);
tkpack(point.but2, poly.but2, side = "left", expand = "TRUE",fill = "x")
tkpack(frame1c, expand = "TRUE", fill = "x")

frame1b <- tkframe(tt, relief = "groove", borderwidth = 2, background = "white")
nettoy.but <- tkbutton(frame1b, text="     Reset selection     " , command=SGfunc);
tkpack(nettoy.but, side = "left", expand = "TRUE", fill = "x")
tkpack(frame1b, expand = "TRUE", fill = "x")


frame2 <- tkframe(tt, relief = "groove", borderwidth = 2, background = "white")
tkpack(tklabel(frame2, text = "Options", font = "Times 14",
foreground = "blue", background = "white"))
tkpack(tklabel(frame2, text = "Spatial contours", font = "Times 11",
foreground = "darkred", background = "white"),tklabel(frame2, text = "Preselected sites", font = "Times 11",
foreground = "darkred", background = "white"), side = "left", fill="x",expand = "TRUE")
tkpack(frame2, expand = "TRUE", fill = "x")

frame2b <- tkframe(tt, relief = "groove", borderwidth = 2, background = "white")
nocou1.but <- tkbutton(frame2b, text="On/Off", command=cartfunc)
noint1.but <- tkbutton(frame2b, text="On/Off", command=fnointer)
tkpack(nocou1.but,noint1.but, side = "left", expand = "TRUE", fill = "x")
tkpack(frame2b, expand = "TRUE", fill = "x")

frame2c <- tkframe(tt, relief = "groove", borderwidth = 2, background = "white")
tkpack(tklabel(frame2c, text = "Bubbles", font = "Times 11",
foreground = "darkred", background = "white"),tklabel(frame2c, text = "Additional graph", font = "Times 11",
foreground = "darkred", background = "white"), side = "left", fill="x",expand = "TRUE")
tkpack(frame2c, expand = "TRUE", fill = "x")

frame2d <- tkframe(tt, relief = "groove", borderwidth = 2, background = "white")
bubble.but <- tkbutton(frame2d, text="On/Off", command=fbubble)
autre.but <- tkbutton(frame2d, text="     OK     " , command=graphfunc)
tkpack(bubble.but,autre.but, side = "left", expand = "TRUE", fill = "x")
tkpack(frame2d, expand = "TRUE", fill = "x")

if(quantiles)
{
frame2e <- tkframe(tt, relief = "groove", borderwidth = 2, background = "white")

slider1(frame2e, refresh.code, names.slide=names.slide,
        borne1, borne2, (borne2 - borne1)/100, alpha)

tkpack(frame2e, expand = "TRUE", fill = "x")
}

frame3 <- tkframe(tt, relief = "groove", borderwidth = 2, background = "white")
tkpack(tklabel(frame3, text = "Exit", font = "Times 14",
foreground = "blue", background = "white"))

quit.but <- tkbutton(frame3, text="Save results", command=quitfunc2);
quit.but2 <- tkbutton(frame3, text="Exit without saving", command=quitfunc);

tkpack(quit.but, quit.but2, side = "left", expand = "TRUE",
        fill = "x")

tkpack(frame3, expand = "TRUE", fill = "x")
}

####################################################
return(invisible())

}