plot3dmap <- function(sf.obj, names.var, box = TRUE, criteria = NULL, carte = NULL,
identify = NULL, cex.lab = 0.8, pch = 16, col = "lightblue3", xlab = "", ylab = "", zlab = "",
axes = FALSE, lablong = "", lablat = "") {
###################################################
########## COMMON to ALL FUNCTIONS in GeoXp
envir <- globalenv()
# Verification of the Spatial Object sf.obj
class.obj <- class(sf.obj)[1]
if(class.obj != "sf")
stop("sf.obj may be a sf object")
# we propose to refind the same arguments used in first version of GeoXp
if (st_geometry_type(sf.obj, by_geometry = F) %in% c("POINT"))
my_coords <- st_coordinates(st_geometry(sf.obj))
else
my_coords <- st_coordinates(st_point_on_surface(st_geometry(sf.obj)))
long <- my_coords[, 1]
lat <- my_coords[, 2]
listvar <- as.data.frame(st_drop_geometry(sf.obj))
listnomvar <- colnames(listvar)
# for identifying the selected sites
if (!is.null(identify) && identify %in% colnames(sf.obj))
label <- sf.obj[[identify]]
else
label <- ""
nointer <- FALSE
nocart <- FALSE
buble <- FALSE
z <- NULL
legmap <- NULL
legends <- list(FALSE, FALSE, "", "")
labvar <- c(xlab, ylab)
graphChoice <- ""
varChoice1 <- ""
varChoice2 <- ""
choix <- ""
method <- ""
listgraph <- c("Histogram", "Barplot", "Scatterplot")
# Is there a Tk window already open ?
if (interactive()) {
if (!exists("GeoXp.open", envir = envir) ||
length(ls(envir = .TkRoot$env, all.names = TRUE)) == 2) {
assign("GeoXp.open", TRUE, envir = envir)
} else {
if (get("GeoXp.open", envir = envir)) {
stop(
"A GeoXp function is already open.
Please, close Tk window before calling a new GeoXp function to avoid conflict between graphics")
} else {
assign("GeoXp.open", TRUE, envir = envir)
}
}
}
if (is.numeric(names.var)) {
if (all(names.var <= ncol(listvar)))
names.var <- listnomvar[names.var]
else
stop("Dimension of names.var is not good")
}
if(!(all(names.var %in% names(sf.obj))))
stop("names.var is not included in the sf object")
var1 <- sf.obj[[names.var[1]]]
var2 <- sf.obj[[names.var[2]]]
var3 <- sf.obj[[names.var[3]]]
var1 <- as.matrix(var1)
var2 <- as.matrix(var2)
var3 <- as.matrix(var3)
lat <- as.matrix(lat)
long <- as.matrix(long)
obs <- vector(mode = "logical", length = length(long))
# for colors in map and new grahics
col2 <- "blue"
col3 <- col[1]
pch2 <- pch[1]
labmod <- ""
# Windows device
if(length(dev.list()) == 0 & options("device") == "RStudioGD")
dev.new()
# for map
dev.new(noRStudioGD = FALSE)
num_carte <- dev.list()[length(dev.list())]
# number of devices
num_supp <- NA
####################################################
# selection d'un point
####################################################
pointfunc <- function() {
quit <- FALSE
dev.set(num_carte)
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 or use ESC",
cex.sub = 0.8, font.sub = 3, col.sub = "red")
while(!quit) {
#selection des points
dev.set(num_carte)
if (nrow(sf.obj) > 100 & st_geometry_type(sf.obj, by_geometry = F) == "POLYGON" & !buble) {
points(long, lat, pch = 16, col = "royalblue")
}
loc <- locator(1)
if (is.null(loc)) {
quit <- TRUE
carte(long = long, lat = lat, obs = obs, sf.obj = sf.obj, num = num_carte, 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 (nrow(sf.obj) > 100 | st_geometry_type(sf.obj, by_geometry = F) == "POINT")
obs <<- selectmap(var1 = long, var2 = lat, obs = obs,
Xpoly = loc[1], Ypoly = loc[2], method = "point")
else {
my_points <- st_as_sf(data.frame(x = loc$x, y = loc$y), coords = c("x", "y"),
crs = st_crs(sf.obj))
def <- as.vector(st_intersects(my_points, sf.obj, sparse = FALSE))
obs[def] <<- !obs[def]
}
# graphiques
if (length(which(obs == TRUE)) == 0 || length(which(obs == TRUE)) == length(obs)) {
if (length(which(obs == TRUE)) == 0)
plot3d(var1[!obs], var2[!obs], var3[!obs],
xlab = xlab, ylab = ylab, zlab = zlab,
col = col, type = "p", size = 5, box = box)
else
plot3d(var1[obs], var2[obs], var3[obs],
xlab = xlab, ylab = ylab, zlab = zlab,
col = "red", type = "p", size = 6, box = box)
} else {
col.prov <- rep(col, length(var1))
col.prov[obs] <- "red"
plot3d(var1, var2, var3,
xlab = xlab, ylab = ylab, zlab = zlab,
col = col.prov, type = "p", size = 5, box = box)
}
carte(long = long, lat = lat, obs = obs, num = num_carte, sf.obj = sf.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)])
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 or use 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 = num_supp, graph = graphChoice, couleurs = col3,
symbol = pch, labvar = c(varChoice1, varChoice2))
}
}
####################################################
# selection d'un polygone
####################################################
polyfunc <- function() {
polyX <- NULL
polyY <- NULL
quit <- FALSE
dev.set(num_carte)
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 or use ESC",
cex.sub = 0.8, font.sub = 3, col.sub = "red")
points(long, lat, pch = 16, col = "royalblue")
while (!quit) {
dev.set(num_carte)
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)
obs <<- selectmap(var1 = long, var2 = lat, obs = obs,
Xpoly = polyX, Ypoly = polyY, method = "poly")
# graphiques
if (length(which(obs == TRUE)) == 0 || length(which(obs == TRUE)) == length(obs)) {
if (length(which(obs == TRUE)) == 0)
plot3d(var1[!obs], var2[!obs], var3[!obs],
xlab = xlab, ylab = ylab, zlab = zlab,
col = col, type = "p", size = 5, box = box)
else
plot3d(var1[obs], var2[obs], var3[obs],
xlab = xlab, ylab = ylab, zlab = zlab,
col = "red", type = "p", size = 6, box = box)
} else {
col.prov <- rep(col, length(var1))
col.prov[obs] <- "red"
plot3d(var1, var2, var3,
xlab = xlab, ylab = ylab, zlab = zlab, col = col.prov,
type = "p", size = 5, box = box)
}
carte(long = long, lat = lat, obs = obs, num = num_carte, sf.obj = sf.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 = num_supp, graph = graphChoice, couleurs = col3,
symbol = pch, labvar = c(varChoice1, varChoice2))
}
}
####################################################
# contour des unites spatiales
####################################################
cartfunc <- function() {
if (length(carte) != 0) {
nocart <<- !nocart
carte(long = long, lat = lat, obs = obs, num = num_carte, sf.obj = sf.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,
num_carte = num_carte)
method <<- res1$method
col2 <<- res1$col2
col3 <<- res1$col3
pch2 <<- res1$pch2
legends <<- res1$legends
labmod <<- res1$labmod
if(is.na(num_supp)) {
dev.new(noRStudioGD = FALSE)
num_supp <<- dev.list()[length(dev.list())]
}
layout(1)
par(mar = c(5.1, 4.1, 4.1, 2.1))
graphique(var1 = listvar[,which(listnomvar == varChoice1)],
var2 = listvar[,which(listnomvar == varChoice2)],
obs = obs, num = num_supp, graph = graphChoice, couleurs = col3,
symbol = pch, labvar = c(varChoice1, varChoice2))
carte(long = long, lat = lat, obs = obs, num = num_carte, sf.obj = sf.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
plot3d(var1, var2, var3,
xlab = xlab, ylab = ylab, zlab = zlab,
col = col, type = "p", size = 5, box = box)
carte(long = long, lat = lat, obs = obs, num = num_carte, sf.obj = sf.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 = num_supp, graph = graphChoice, couleurs = col3,
symbol = pch, labvar = c(varChoice1, varChoice2))
}
####################################################
# quitter l'application
####################################################
quitfunc <- function(){
tkdestroy(tt)
assign("GeoXp.open", FALSE, envir = envir)
close3d()
dev.off(num_carte)
if (!is.na(num_supp))
dev.off(num_supp)
}
quitfunc2 <- function() {
fig_save <- "fig_GeoXp.pdf"
map_save <- "map_GeoXp.pdf"
k <- 1
while(file.exists(fig_save)) {
fig_save <- paste("fig_GeoXp", "_", k, ".pdf", sep = "")
k <- k + 1
}
rgl.postscript(fig_save,"pdf")
k <- 1
while(file.exists(map_save)) {
map_save <- paste("map_GeoXp", "_", k, ".pdf", sep = "")
k <- k + 1
}
pdf(map_save)
carte(long = long, lat = lat, obs = obs, sf.obj = sf.obj, num = dev.list()[length(dev.list())], 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)])
dev.off()
if(!is.na(num_supp)) {
fig_supp <- "fig_supp_GeoXp.pdf"
k <- 1
while(file.exists(fig_supp)) {
fig_supp <- paste("fig_supp_GeoXp", "_", k, ".pdf", sep = "")
k <- k + 1
}
pdf(fig_supp)
graphique(var1 = listvar[, which(listnomvar == varChoice1)],
var2 = listvar[, which(listnomvar == varChoice2)],
obs = obs, num = dev.list()[length(dev.list())], graph = graphChoice, couleurs = col3,
symbol = pch, labvar = c(varChoice1, varChoice2))
dev.off()
}
tkdestroy(tt)
assign("GeoXp.open", FALSE, envir = envir)
cat("Results have been saved in last.select object \n")
cat("Map has been saved in", map_save, "\n")
cat("Figure has been saved in", fig_save, "\n")
if(!is.na(num_supp))
cat("Supplemental figure has been saved in", fig_supp, "\n")
assign("last.select", which(obs), envir = envir)
dev.off(num_carte)
close3d()
if(!is.na(num_supp))
dev.off(num_supp)
}
####################################################
# Open a no interactive selection
####################################################
fnointer <- function() {
if (length(criteria) != 0) {
nointer <<- !nointer
carte(long = long, lat = lat, obs = obs, sf.obj = sf.obj, num = num_carte, 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, num_carte = num_carte)
buble <<- res2$buble
legends <<- res2$legends
z <<- res2$z
legmap <<- res2$legmap
carte(long = long, lat = lat, obs = obs, sf.obj = sf.obj, num = num_carte, 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)])
}
####################################################
# graphiques
####################################################
carte(long = long, lat = lat, obs = obs, sf.obj = sf.obj, num = num_carte, 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)])
par3d(windowRect = c(0, 32, 512, 544), userMatrix = rotationMatrix(5*pi/180, 0, 1, 0) %*% par3d("userMatrix"), family = "sans")
bg3d(color = "white")
plot3d(var1, var2, var3,
xlab = xlab, ylab = ylab, zlab = zlab,
xlim = range(var1), ylim = range(var2), zlim = range(var3),
col = col, size = 5, type = "n", box = box)
plot3d(var1, var2, var3,
xlab = xlab, ylab = ylab, zlab = zlab,
xlim = range(var1), ylim = range(var2), zlim = range(var3),
col = col, size = 5, type = "p", box = FALSE, add = TRUE)
####################################################
# creation de la boite de dialogue
####################################################
if (interactive()) {
fontheading <- tkfont.create(family = "times", size = 14, weight = "bold")
tt <- tktoplevel()
tkwm.title(tt, "plot3dmap")
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 = pointfunc)
poly.but <- tkbutton(frame1a, text = "Selection by polygon ", command = polyfunc)
tkpack(point.but, poly.but, side = "left", expand = "TRUE", fill = "x")
tkpack(frame1a, 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")
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())
}
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