R version 4.5.0 RC (2025-04-04 r88113 ucrt) -- "How About a Twenty-Six"
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> library(adegraphics)
Registered S3 methods overwritten by 'adegraphics':
  method         from
  biplot.dudi    ade4
  kplot.foucart  ade4
  kplot.mcoa     ade4
  kplot.mfa      ade4
  kplot.pta      ade4
  kplot.sepan    ade4
  kplot.statis   ade4
  scatter.coa    ade4
  scatter.dudi   ade4
  scatter.nipals ade4
  scatter.pco    ade4
  score.acm      ade4
  score.mix      ade4
  score.pca      ade4
  screeplot.dudi ade4
> pdf("add.pdf")
> set.seed(40)
> 
> ########################### add.ADEg ##############################
> 
> data(granulo, package = "ade4")
> df <- data.frame(t(apply(granulo$tab, 1, function(x) x / sum(x))))
> pca <- ade4::dudi.pca(df, scal = FALSE, scan = FALSE)
> 
> g1 <- s.arrow(ade4::dudi.pca(data.frame(df), scan = F, nf = 2)$co)
> g2 <- s.label(pca$li, plabels.cex = 0.5, plabels.col = "blue", plot = F)
> g3 <- add.ADEg(g2)
> g4 <- s.label(pca$c1, plabels.col = "red", add = T)
> 
> g5 <- s.arrow(pca$c1, plabels.cex = 1.5, plot = FALSE)
> g6 <- ADEgS(list(g1 = g1, g5 = g5), layout = c(1, 2))
> update(g6, pback.col = "lightblue", g1.plabels.cex = 2, g5.plabels.col = "red")
> 
> 
> ############################## addhist ##############################
> dfxy1 <- matrix(rnorm(200), ncol = 2)
> gh1 <- s.label(dfxy1)
> gh2 <- addhist(gh1)
> 
> dfxy2 <- dfxy1
> dfxy2[, 2] <- dfxy2[, 2] + rnorm(100, 2)
> gh3 <- s.label(dfxy2)
> gh4 <- addhist(gh3, plot.polygon = list(col = "red"))
> 
> data(rpjdl, package = "ade4")
> coa1 <- ade4::dudi.coa(rpjdl$fau, scannf = FALSE, nf = 4)
> gh5 <- s.label(coa1$li)
> gh6 <- addhist(gh5)
> 
> 
> ############################## addtext ##############################
> # on a ADEg
> addtext(g1, -1, 1, "Data Granulo", plabels.cex = 1.5, plabels.col = "red")
> addtext(g1, -1, 1, c("Data", "Granulo"), plabels.cex = 1.5, plabels.col = c("red", "blue")) # the two labels are superposed
> addtext(g1, -1, 1, c("Data", "Granulo"), plabels.cex = 1.5, plabels.col = "red") # the two labels are superposed
> 
> addtext(g1, c(-1, -0.5), 1, "Data Granulo", plabels.cex = 1.5, plabels.col = c("red", "blue"))
> addtext(g1, c(-1, -0.5), 1, c("Data", "Granulo"), plabels.cex = 1.5, plabels.col = c("red", "blue"))
> 
> addtext(g1, -1, c(1, 0.9), c("Data", "Granulo"), plabels.cex = 1.5, plabels.col = "red")
> addtext(g1, -1, c(1, 0.9), c("Data", "Granulo"), plabels.cex = c(1.5, 2), plabels.col = "red")
> 
> data(dunedata, package = "ade4")
> afc1 <- ade4::dudi.coa(dunedata$veg, scannf = FALSE)
> g7 <- table.value(dunedata$veg, symbol = "circle", ppoints.cex = 0.5, plot = FALSE)
> addtext(g7, 1, 20, "A", plabels.srt = 45, plabels.boxes.draw = FALSE)
> 
> # on a ADEgS: juxtaposition
> addtext(g6, 0.5, 0.5, "Text added", plabels.col = "blue", which = 1)
> addtext(g6, 0.5, 0.5, "Text added", plabels.col = c("blue", "green"), which = 2)
> addtext(g6, 0.5, 0.5, "Text added", plabels.col = c("green4", "blue"), which = 2)
> addtext(g6, 0.5, 0.5, "Text added", plabels.col = "blue", which = 1:2)
> addtext(g6, 0.5, 0.5, "Text added", plabels.col = c("green4", "blue"))
> addtext(g6, c(0.7, -0.5), c(0.2, -0.4), "Text added", plabels.col = "blue", plabels.cex = 1.2, which = 1:2)
> addtext(g6, c(0.7, -0.5), c(0.2, -0.4), "Text added", plabels.cex = c(0.5, 1.5), plabels.col = c("blue", "green4"))
> 
> xy2 <- cbind.data.frame(x = runif(200, -1, 1), y = runif(200, -2, 2), y2 = runif(200, -0.5, 0.5))
> fac2 <- factor(xy2$x > 0) 
> g9 <- s.class(xy2, fac = fac2, xax = 1, yax = 2:3, plot = FALSE)
> addtext(g9, 0, 0, "A", plabels.col = "red", plabels.cex = 2)
> addtext(g9, c(-2.1, -1.07), c(2, 1), c("A", "B"), plabels.col ="red", plabels.cex = 2, which = 1:2)
> addtext(g9, c(-2.1, -1.07), c(2, 1), c("A", "B"), plabels.col = c("green4", "red"), plabels.cex = c(3, 2), which = 1:2)
> 
> # on a ADEgS: facets
> xy <- cbind.data.frame(x = runif(200, -1, 1), y = runif(200, -1, 1))
> posi <- factor(xy$x > 0) : factor(xy$y > 0)
> g10 <- s.class(xy, fac = posi, facets = posi, pellipses.col = 1:4, plabels.cex = 0, plegend.drawKey = FALSE, psub.cex = 0, plot = FALSE)
> addtext(g10, c(0.5, 0.5, -0.5, -0.5), c(0.5, -0.5), levels(posi), plabels.cex = 2, plabels.col = 1:4)
> 
> 
> ############################## addline ##############################
> # on a 2D plot
> g11 <- s.label(cbind(rnorm(100), rnorm(100)), plot = FALSE)
> addline(g11, 0, 1, plines = list(col = "red", lwd = 2, lty = 2))
> addline(g11, h = 1, plines.col = "chartreuse4", plines.lwd = 3)
> addline(g11, v = c(-1, 1), plines.col = "cadetblue", plines.lwd = 3)
> 
> # on a 1D plot
> g12 <- s1d.label(rnorm(10), plot = FALSE)
> addline(g12, v = 1, plines.col = "chartreuse4", plines.lwd = 3)
> 
> # on a ADEgS: juxtaposition
> g13 <- ADEgS(c(g11, g11), plot = FALSE)
> addline(g13, 0, 1, which = 1, plines.col = "red")
> addline(g13, 0, 1, which = 2, plines.col = "red")
> addline(g13, 0, 1, which = 1:2, plines.col = "red")
> addline(g13, 0, 1, plines.col = "red")
> addline(g13, h = 1, plines.col = "red")
> addline(g13, h = c(1, -1), plines.col = "red")
> addline(g13, v = c(-1, 1), plines.col = "red")
> addline(g13, v = c(-1, 1), plines.col = 2:3)
> addline(g13, c(0.7, -0.5), c(0.2, -0.4), which = 1:2, plines.col = "red")
> addline(g13, c(0.7, -0.5), c(0.2, -0.4), which = 1, plines.col = "red")
> addline(g13, 0.7, 0.2, which = 1, plines.col = "red")
> addline(g13, 0.7, -0.5, which = 1, plines.col = "red")
> 
> xy2 <- cbind.data.frame(x = runif(200, -1, 1), y = runif(200, -2, 2), y2 = runif(200, -0.5, 0.5))
> fac2 <- factor(xy2$x > 0) 
> g9 <- s.class(xy2, fac = fac2, xax = 1, yax = 2:3, plot = FALSE)
> addline(g9, 1, 0, "A", plines.col = "red", plabels.cex = 2)
Warning messages:
1: In panel.abline(a = a, b = b, h = h, v = v, lwd = params$lwd, lty = params$lty,  :
  NAs introduced by coercion
2: In panel.abline(a = a, b = b, h = h, v = v, lwd = params$lwd, lty = params$lty,  :
  NAs introduced by coercion
> addline(g9, c(-2.1, -1.07), c(2, 1), plines.col ="red", which = 1:2)
> addline(g9, c(-2.1, -1.07), c(2, 1), plines.col = c("green4", "red"))
> 
> # on a ADEgS: facets
> xy <- cbind.data.frame(x = runif(200, -1, 1), y = runif(200, -1, 1))
> posi <- factor(xy$x > 0) : factor(xy$y > 0)
> g10 <- s.class(xy, fac = posi, facets = posi, pellipses.col = 1:4, plabels.cex = 0, plegend.drawKey = FALSE, psub.cex = 0, plot = FALSE)
> addline(g10, 0, c(0.5, -0.5), plines.col = 1:4)
> 
> 
> ############################## addpoint ##############################
> # on a 2D plot
> g11 <- s.label(cbind(rnorm(100), rnorm(100)), ylab = "y axis label", 
+                paxes.draw = TRUE, plot = FALSE)
> addpoint(g11, 2, 2, ppoints.col = "coral", ppoints.pch = "*", ppoints.cex = 4)
> addpoint(g11, c(1, 2), c(1, 2), ppoints.col = "brown2")
> addpoint(g11, 1, c(1, 2), ppoints.col = "cyan3")
> 
> # on a 1D plot
> g12 <- s1d.density(rnorm(1000), paxes.draw = TRUE, plot = FALSE)
> addpoint(g12, 2, 0, ppoints.col = "brown4", ppoints.cex = 3)
> 
> g12 <- s1d.density(rnorm(1000), plot = FALSE, ylab = "y axis label")
> addpoint(g12, 2, 0, ppoints.col = "brown4", ppoints.cex = 3)
> 
> # on a ADEgS: juxtaposition
> g13 <- ADEgS(c(g11, g11), plot = FALSE)
> addpoint(g13, 2, 2, which = 1, ppoints.col = "cyan3")
> addpoint(g13, 2, 2, which = 2, ppoints.col = "cyan3")
> addpoint(g13, 2, 2, which = 1:2, ppoints.col = "cyan3")
> addpoint(g13, 2, 2, ppoints.col = "cyan3")
> addpoint(g13, c(1, 2), 2, ppoints.col = "cyan3")
> addpoint(g13, 2, c(1, 2), ppoints.col = "cyan3")
> 
> xy2 <- cbind.data.frame(x = runif(200, -1, 1), y = runif(200, -2, 2), y2 = runif(200, -0.5, 0.5))
> fac2 <- factor(xy2$x > 0) 
> g9 <- s.class(xy2, fac = fac2, xax = 1, yax = 2:3, plot = FALSE)
> addpoint(g9, 1, 0, ppoints.col = "red", ppoints.cex = 2)
> addpoint(g9, c(1, -1), 0, ppoints.col = "red", ppoints.cex = 2)
> addpoint(g9, 0, c(1, -1), ppoints.col = "red", ppoints.cex = 2)
> 
> # on a ADEgS: facets
> xy <- cbind.data.frame(x = runif(200, -1, 1), y = runif(200, -1, 1))
> posi <- factor(xy$x > 0) : factor(xy$y > 0)
> g10 <- s.class(xy, fac = posi, facets = posi, pellipses.col = 1:4, plabels.cex = 0, plegend.drawKey = FALSE, psub.cex = 0, plot = FALSE)
> addpoint(g10, 0, c(0.5, -0.5), ppoints.col = 1:4, ppoints.cex = 3)
> 
> 
> ############################## addsegment ##############################
> # on a 2D plot
> g11 <- s.label(cbind(rnorm(100), rnorm(100)), paxes.draw = TRUE, plot = FALSE)
> addsegment(g11, 0, 2, 0, -2, plines = list(col = "brown2", lwd = 3, lty = 2))
> addsegment(g11, c(0, 1), 2, 0, -2, plines = list(col = "brown2", lwd = 3, lty = 2))
> addsegment(g11, c(0, 1), 2, c(0, 1), -2, plines = list(col = c("cyan3", "brown2"), lwd = 3, lty = 2))
> addsegment(g11, -2, -2, 2, 2, plines = list(col = "brown2", lwd = 3, lty = 2))
> addsegment(g11, -2, 2, 2, -2, plines = list(col = "cyan3", lwd = 3, lty = 2))
> 
> g12 <- s.label(cbind(rnorm(100), rnorm(100)), ylab = "y axis label", plot = FALSE)
> addsegment(g12, 0, 2, 0, -2, plines = list(col = "brown2", lwd = 3, lty = 2))
> addsegment(g12, -2, -2, 2, 2, plines = list(col = "brown2", lwd = 3, lty = 2))
> addsegment(g12, -2, 2, 2, -2, plines = list(col = "cyan3", lwd = 3, lty = 2))
> 
> # on a 1D plot
> g13 <- s1d.density(rnorm(1000), paxes.draw = TRUE, ylab = "ylab", plot = FALSE)
> addsegment(g13, 2, 0, 2, 0.2, plines.col = 1, plines.lwd = 3)
> 
> # on a ADEgS: juxtaposition
> g14 <- ADEgS(c(g11, g11), plot = FALSE)
> addsegment(g14, 1, 2, 1, -2, which = 1, plines.col = "brown2")
> addsegment(g14, 1, 2, 1, -2, which = 2, plines.col = "brown2")
> addsegment(g14, c(0, 1), 2, c(0, 1), -2, which = 1:2, plines.col = "brown2")
> addsegment(g14, 1, 2, c(0, 1), -2, which = 1:2, plines.col = "brown2")
> addsegment(g14, 1, 2, 1, -2, plines.col = "brown2")
> 
> xy2 <- cbind.data.frame(x = runif(200, -1, 1), y = runif(200, -2, 2), y2 = runif(200, -0.5, 0.5))
> fac2 <- factor(xy2$x > 0) 
> g9 <- s.class(xy2, fac = fac2, xax = 1, yax = 2:3, plot = FALSE)
> addsegment(g9, 1, 0, 1, 0.5, plines.col = "red", plines.lwd = 2)
> addsegment(g9, 1, -1, 0, 1, plines.col = "red", plines.lwd = 2)
> addsegment(g9, 0, 1, -1, 1, plines.col = "red", plines.lwd = 2)
> 
> # on a ADEgS: facets
> xy <- cbind.data.frame(x = runif(200, -1, 1), y = runif(200, -1, 1))
> posi <- factor(xy$x > 0) : factor(xy$y > 0)
> g10 <- s.class(xy, fac = posi, facets = posi, pellipses.col = 1:4, plabels.cex = 0, plegend.drawKey = FALSE, psub.cex = 0, plot = FALSE)
> addsegment(g10, c(-0.5, 0.5), c(0.5, -0.5), c(-0.5, 0.5), 1, plines.col = 1:4, plines.lwd = 3)
> 
> proc.time()
   user  system elapsed 
  13.46    0.25   13.75