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Plot individual plots along a pair of functional axes into a unique graph

Source: R/plot_multidim_layers.R
panels.to.patchwork.Rd

This function gathers panels into a unique patchwork graph with caption.

Usage

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.

Value

A unique ggplot object gathering functional panels and caption.

Author

Camille Magneville and Sebastien Villeger

Examples

## 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)
#> [1] "Running w.type=equal on groups=c(Size)"
#> [1] "Running w.type=equal on groups=c(Plant)"
#> [1] "Running w.type=equal on groups=c(Climate)"
#> [1] "Running w.type=equal on groups=c(Seed)"
#> [1] "Running w.type=equal on groups=c(Sugar)"
#> [1] "Running w.type=equal on groups=c(Use,Use,Use)"
  
# 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)
#> basket_1 done 10%
#> basket_2 done 20%
#> basket_3 done 30%
#> basket_4 done 40%
#> basket_5 done 50%
#> basket_6 done 60%
#> basket_7 done 70%
#> basket_8 done 80%
#> basket_9 done 90%
#> basket_10 done 100%

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