diff --git a/vignettes/landscapes.Rmd b/vignettes/landscapes.Rmd index 70d7a587..b9e23050 100644 --- a/vignettes/landscapes.Rmd +++ b/vignettes/landscapes.Rmd @@ -115,9 +115,9 @@ A variety of R add-on packages facilitate three-dimensional plots. ```{r plot-3d, message = FALSE} if (requireNamespace("plotly", quietly = TRUE)) { - library("plotly", quietly = TRUE) - fig <- plot_ly(x = x, y = y, z = z) - fig <- fig %>% add_surface() + # Don't attach plotly: it would mask `graphics::layout()` in later vignettes + fig <- plotly::plot_ly(x = x, y = y, z = z) + fig <- plotly::add_surface(fig) fig } else { print("Run `install.packages('plotly')` to view this output") diff --git a/vignettes/treespace.Rmd b/vignettes/treespace.Rmd index 62e2bbec..3c18cdfe 100644 --- a/vignettes/treespace.Rmd +++ b/vignettes/treespace.Rmd @@ -293,7 +293,7 @@ plotSeq <- matrix(0, nDim, nDim) plotSeq[upper.tri(plotSeq)] <- seq_len(nDim * (nDim - 1) / 2) plotSeq <- t(plotSeq[-nDim, -1]) plotSeq[nDim * 1:3] <- (nDim * (nDim - 1) / 2) + 1:3 -layout(plotSeq) +graphics::layout(plotSeq) par(mar = rep(0.1, 4)) for (i in 2:nDim) for (j in seq_len(i - 1)) {