# Plot individual plots along a pair of functional axes into a unique graph This function gathers panels into a unique `patchwork` graph with caption. ```r panels.to.patchwork(panels, plot_caption) ``` ## Arguments - `panels`: a list of ggplot objects illustrating an index on two given functional axes. There must be either one, three or six ggplot objects given the number of studied functional axes. - `plot_caption`: a ggplot object illustrating the caption of the final patchwork plot. ## Returns A unique ggplot object gathering functional panels and caption. ## Examples ```r ## Retrieve FRic plot: # Load Species*Traits dataframe: data("fruits_traits", package = "mFD") # Load Assemblages*Species dataframe: data("baskets_fruits_weights", package = "mFD") # Load Traits categories dataframe: data("fruits_traits_cat", package = "mFD") # Compute functional distance sp_dist_fruits <- mFD::funct.dist(sp_tr = fruits_traits, tr_cat = fruits_traits_cat, metric = "gower", scale_euclid = "scale_center", ordinal_var = "classic", weight_type = "equal", stop_if_NA = TRUE) # Compute functional spaces quality to retrieve species coordinates matrix: fspaces_quality_fruits <- mFD::quality.fspaces(sp_dist = sp_dist_fruits, maxdim_pcoa = 10, deviation_weighting = "absolute", fdist_scaling = FALSE, fdendro = "average") # Retrieve species coordinates matrix: sp_faxes_coord_fruits <- fspaces_quality_fruits$details_fspaces$sp_pc_coord # Retrieve species coordinates matrix for the assemblage "basket_1": sp_filter <- mFD::sp.filter(asb_nm = c("basket_1"), sp_faxes_coord = sp_faxes_coord_fruits, asb_sp_w = baskets_fruits_weights) sp_faxes_coord_fruits_b1 <- sp_filter$`species coordinates` # Reduce it to the two studed axes: PC1 and PC2: sp_faxes_coord_fruits_b1_2D <- sp_faxes_coord_fruits_b1[, c("PC1", "PC2")] # Set faxes limits: # set range of axes if c(NA, NA): range_sp_coord_fruits <- range(sp_faxes_coord_fruits) range_faxes_lim <- range_sp_coord_fruits + c(-1, 1)*(range_sp_coord_fruits[2] - range_sp_coord_fruits[1]) * 0.05 # Retrieve the background plot: ggplot_bg_fruits <- mFD::background.plot( range_faxes = range_faxes_lim, faxes_nm = c("PC 1", "PC 2"), color_bg = "grey90") # Retrieve vertices names: vert_nm_fruits <- vertices(sp_faxes_coord_fruits_b1_2D, order_2D = TRUE, check_input = TRUE) # Plot in white the convex hull of all fruits species: ggplot_fric <- mFD::fric.plot( ggplot_bg = ggplot_bg_fruits, asb_sp_coord2D = list(basket_1 = sp_faxes_coord_fruits_b1_2D), asb_vertices_nD = list(basket_1 = vert_nm_fruits), plot_sp = TRUE, color_ch = c("basket_1" = "black"), fill_ch = c("basket_1" = "white"), alpha_ch = c("basket_1" = 0.3), size_sp = c("basket_1" = 1), shape_sp = c("basket_1" = 16), color_sp = c("basket_1" = "red"), fill_sp = c("basket_1" = "red"), size_vert = c("basket_1" = 1), color_vert = c("basket_1" = "red"), fill_vert = c("basket_1" = "red"), shape_vert = c("basket_1" = 16)) ggplot_fric ## Create a caption summing up FRic values # retrieve values to plot: top_fric <- c("Functional richness", "basket_1", "") asb_fd_ind <- alpha_fd_indices_fruits <- mFD::alpha.fd.multidim( sp_faxes_coord = sp_faxes_coord_fruits[ , c("PC1", "PC2", "PC3", "PC4")], asb_sp_w = baskets_fruits_weights, ind_vect = c("fric"), scaling = TRUE, check_input = TRUE, details_returned = TRUE) values_fric <- c(round(asb_fd_ind$functional_diversity_indices["basket_1", "fric"], 3), "") # customize position of texts in the plot: spread_faxes <- (range_sp_coord_fruits[2] - range_sp_coord_fruits[1]) hh <- c(1, 2.5, 4, 5.5) vv <- 0.3 # plot window: x <- NULL y <- NULL plot_caption <- ggplot2::ggplot(data.frame(x = range_sp_coord_fruits, y = range_sp_coord_fruits), ggplot2::aes(x = x, y = y)) + ggplot2::scale_x_continuous(limits = range_sp_coord_fruits, expand = c(0, 0)) + ggplot2::scale_y_continuous(limits = range_sp_coord_fruits, expand = c(0, 0)) + ggplot2::theme_void() + ggplot2::theme(legend.position = "none") + ggplot2::geom_rect(xmin = range_sp_coord_fruits[1], xmax = range_sp_coord_fruits[2], ymin = range_sp_coord_fruits[1], ymax = range_sp_coord_fruits[2], fill = "white", colour ="black") # plot names of index and of assemblages: h <- NULL v <- NULL top <- NULL x <- NULL y <- NULL plot_caption <- plot_caption + ggplot2::geom_text(data = data.frame( h = range_sp_coord_fruits[1] + spread_faxes * 0.15 * hh[c(1,3:4)], v = range_sp_coord_fruits[2] - spread_faxes * rep(0.2, 3), top = top_fric), ggplot2::aes(x = h, y = v, label = top), size = 3, hjust = 0.5, fontface = "bold") # plot FRic values: values_lab <- NULL data_caption <- data.frame( h = range_sp_coord_fruits[1] + spread_faxes * 0.15 * hh[2:4], v = range_sp_coord_fruits[2] - spread_faxes*rep(vv, 3), values_lab = c("FRic", values_fric)) plot_caption <- plot_caption + ggplot2::geom_text(data = data_caption, ggplot2::aes(x = h, y = v, label = values_lab), size = 3, hjust = 0.5, fontface = "plain") ## Create patchwork: patchwork_fric <- mFD::panels.to.patchwork(list(ggplot_fric), plot_caption) patchwork_fric ``` ## Author(s) Camille Magneville and Sebastien Villeger

panels.to.patchwork function