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inst/doc/Customised_plots.R
In mFD: Compute and Illustrate the Multiple Facets of Functional Diversity
## -----------------------------------------------------------------------------
# Load data:
data("baskets_fruits_weights", package = "mFD")
# Display the table:
knitr::kable(as.data.frame(baskets_fruits_weights[1:6, 1:6]),
centering = TRUE,
caption = "Species x assemblages matrix based on the **fruits** dataset")
## -----------------------------------------------------------------------------
# Load data:
data("fruits_traits", package = "mFD")
# Remove fuzzy traits in this tutorial:
fruits_traits <- fruits_traits[ , -c(6:8)]
# Display the table:
knitr::kable(head(fruits_traits),
caption = "Species x traits data frame")
## -----------------------------------------------------------------------------
# Load data:
data("fruits_traits_cat", package = "mFD")
# Remove fuzzy traits in this tutorial:
fruits_traits_cat <- fruits_traits_cat[-c(6:8), ]
# Thus remove the "fuzzy_name" column:
fruits_traits_cat <- fruits_traits_cat[ , -3]
# Display the table:
knitr::kable(head(fruits_traits_cat),
caption = "Traits types based on **fruits & baskets** dataset")
## ----results = "hide"---------------------------------------------------------
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)
## ----results = "hide", message = FALSE----------------------------------------
# Quality of functional spaces:
fspaces_quality_fruits <- mFD::quality.fspaces(
sp_dist = sp_dist_fruits,
maxdim_pcoa = 10,
deviation_weighting = "absolute",
fdist_scaling = FALSE,
fdendro = "average")
# retrieve species (fruits) coordinates in the 4D space (see General tutorial):
sp_faxes_coord_fruits <- fspaces_quality_fruits$"details_fspaces"$"sp_pc_coord"
## ----results = "hide", message = FALSE----------------------------------------
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)
## -----------------------------------------------------------------------------
# Compute the range of functional axes:
range_sp_coord <- range(sp_faxes_coord_fruits)
# Based on the range of species coordinates values, compute a nice range ...
# ... for functional axes:
range_faxes <- range_sp_coord +
c(-1, 1) * (range_sp_coord[2] - range_sp_coord[1]) * 0.05
range_faxes
## ----fig.height = 3, fig.width = 5, fig.align = "center"----------------------
# get species coordinates along the two studied axes:
sp_faxes_coord_xy <- sp_faxes_coord_fruits[, c("PC1", "PC2")]
# Plot background with grey backrgound:
plot_k <- mFD::background.plot(range_faxes = range_faxes,
faxes_nm = c("PC1", "PC2"),
color_bg = "grey95")
plot_k
## -----------------------------------------------------------------------------
# Retrieve vertices coordinates along the two studied functional axes:
vert <- mFD::vertices(sp_faxes_coord = sp_faxes_coord_xy,
order_2D = FALSE,
check_input = TRUE)
## ----fig.height = 3, fig.width = 5, fig.align = "center"----------------------
plot_sp_vert <- mFD::pool.plot(ggplot_bg = plot_k,
sp_coord2D = sp_faxes_coord_xy,
vertices_nD = vert,
plot_pool = TRUE,
color_pool = "black",
fill_pool = NA,
alpha_ch = 0.8,
color_ch = NA,
fill_ch = "white",
shape_pool = 3,
size_pool = 0.8,
shape_vert = 16,
size_vert = 1,
color_vert = "green",
fill_vert = "green")
plot_sp_vert
## ----fig.height = 3, fig.width = 5, fig.align = "center"----------------------
plot_k <- mFD::pool.plot(ggplot_bg = plot_k,
sp_coord2D = sp_faxes_coord_xy,
vertices_nD = vert,
plot_pool = FALSE,
color_pool = NA,
fill_pool = NA,
alpha_ch = 0.8,
color_ch = "white",
fill_ch = "white",
shape_pool = NA,
size_pool = NA,
shape_vert = NA,
size_vert = NA,
color_vert = NA,
fill_vert = NA)
plot_k
## -----------------------------------------------------------------------------
# basket_1:
## filter species from basket_1:
sp_filter_basket1 <- mFD::sp.filter(asb_nm = c("basket_1"),
sp_faxes_coord = sp_faxes_coord_xy,
asb_sp_w = baskets_fruits_weights)
## get species coordinates (basket_1):
sp_faxes_coord_basket1 <- sp_filter_basket1$`species coordinates`
# basket_6:
## filter species from basket_6:
sp_filter_basket6 <- mFD::sp.filter(asb_nm = c("basket_6"),
sp_faxes_coord = sp_faxes_coord_xy,
asb_sp_w = baskets_fruits_weights)
## get species coordinates (basket_6):
sp_faxes_coord_basket6 <- sp_filter_basket6$`species coordinates`
# basket_10:
## filter species from basket_10:
sp_filter_basket10 <- mFD::sp.filter(asb_nm = c("basket_10"),
sp_faxes_coord = sp_faxes_coord_xy,
asb_sp_w = baskets_fruits_weights)
## get species coordinates (basket_10):
sp_faxes_coord_basket10 <- sp_filter_basket10$`species coordinates`
## -----------------------------------------------------------------------------
sp_faxes_coord_basket1
## -----------------------------------------------------------------------------
# basket_1:
vert_nm_basket1 <- mFD::vertices(sp_faxes_coord = sp_faxes_coord_basket1,
order_2D = TRUE,
check_input = TRUE)
# basket_6:
vert_nm_basket6 <- mFD::vertices(sp_faxes_coord = sp_faxes_coord_basket6,
order_2D = TRUE,
check_input = TRUE)
# basket_10:
vert_nm_basket10 <- mFD::vertices(sp_faxes_coord = sp_faxes_coord_basket10,
order_2D = TRUE,
check_input = TRUE)
## ----fig.height = 3, fig.width = 5, fig.align = "center"----------------------
plot_try <- mFD::fric.plot(ggplot_bg = plot_k,
asb_sp_coord2D = list("basket_1" = sp_faxes_coord_basket1,
"basket_6" = sp_faxes_coord_basket6,
"basket_10" = sp_faxes_coord_basket10),
asb_vertices_nD = list("basket_1" = vert_nm_basket1,
"basket_6" = vert_nm_basket6,
"basket_10" = vert_nm_basket10),
plot_sp = FALSE,
color_ch = NA,
fill_ch = c("basket_1" = "#1c9099",
"basket_6" = "#67a9cf",
"basket_10" = "#d0d1e6"),
alpha_ch = c("basket_1" = 0.4,
"basket_6" = 0.4,
"basket_10" = 0.4),
shape_sp = NA,
size_sp = NA,
color_sp = NA,
fill_sp = NA,
shape_vert = NA,
size_vert = NA,
color_vert = NA,
fill_vert = NA)
plot_try
## ----fig.height = 3, fig.width = 5, fig.align = "center"----------------------
plot_try <- mFD::fric.plot(ggplot_bg = plot_k,
asb_sp_coord2D = list("basket_1" = sp_faxes_coord_basket1,
"basket_6" = sp_faxes_coord_basket6,
"basket_10" = sp_faxes_coord_basket10),
asb_vertices_nD = list("basket_1" = vert_nm_basket1,
"basket_6" = vert_nm_basket6,
"basket_10" = vert_nm_basket10),
plot_sp = FALSE,
color_ch = c("basket_1" = "#7a0177",
"basket_6" = "#c51b8a",
"basket_10" = "#fa9fb5"),
fill_ch = c("basket_1" = "#1c9099",
"basket_6" = "#67a9cf",
"basket_10" = "#d0d1e6"),
alpha_ch = c("basket_1" = 0.4,
"basket_6" = 0.4,
"basket_10" = 0.4),
shape_sp = NA,
size_sp = NA,
color_sp = NA,
fill_sp = NA,
shape_vert = NA,
size_vert = NA,
color_vert = NA,
fill_vert = NA)
plot_try
## ----fig.height = 3, fig.width = 5, fig.align = "center"----------------------
plot_try <- mFD::fric.plot(ggplot_bg = plot_k,
asb_sp_coord2D = list("basket_1" = sp_faxes_coord_basket1,
"basket_6" = sp_faxes_coord_basket6,
"basket_10" = sp_faxes_coord_basket10),
asb_vertices_nD = list("basket_1" = vert_nm_basket1,
"basket_6" = vert_nm_basket6,
"basket_10" = vert_nm_basket10),
plot_sp = TRUE,
color_ch = NA,
fill_ch = c("basket_1" = "#1c9099",
"basket_6" = "#67a9cf",
"basket_10" = "#d0d1e6"),
alpha_ch = c("basket_1" = 0.4,
"basket_6" = 0.4,
"basket_10" = 0.4),
shape_sp = c("basket_1" = 21,
"basket_6" = 22,
"basket_10" = 24),
size_sp = c("basket_1" = 2,
"basket_6" = 2,
"basket_10" = 2),
color_sp = c("basket_1" = "#1c9099",
"basket_6" = "#67a9cf",
"basket_10" = "#d0d1e6"),
fill_sp = c("basket_1" = "#1c9099",
"basket_6" = "#67a9cf",
"basket_10" = "#d0d1e6"),
shape_vert = c("basket_1" = 21,
"basket_6" = 22,
"basket_10" = 24),
size_vert = c("basket_1" = 2,
"basket_6" = 2,
"basket_10" = 2),
color_vert = c("basket_1" = "#1c9099",
"basket_6" = "#67a9cf",
"basket_10" = "#d0d1e6"),
fill_vert = c("basket_1" = "#1c9099",
"basket_6" = "#67a9cf",
"basket_10" = "#d0d1e6"))
plot_try
## ----fig.height = 3, fig.width = 5, fig.align = "center"----------------------
plot_try <- mFD::fric.plot(ggplot_bg = plot_k,
asb_sp_coord2D = list("basket_1" = sp_faxes_coord_basket1,
"basket_6" = sp_faxes_coord_basket6,
"basket_10" = sp_faxes_coord_basket10),
asb_vertices_nD = list("basket_1" = vert_nm_basket1,
"basket_6" = vert_nm_basket6,
"basket_10" = vert_nm_basket10),
plot_sp = TRUE,
color_ch = NA,
fill_ch = c("basket_1" = "#1c9099",
"basket_6" = "#67a9cf",
"basket_10" = "#d0d1e6"),
alpha_ch = c("basket_1" = 0.4,
"basket_6" = 0.4,
"basket_10" = 0.4),
shape_sp = c("basket_1" = 21,
"basket_6" = 22,
"basket_10" = 24),
size_sp = c("basket_1" = 2,
"basket_6" = 2,
"basket_10" = 2),
color_sp = c("basket_1" = "#1c9099",
"basket_6" = "#67a9cf",
"basket_10" = "#d0d1e6"),
fill_sp = c("basket_1" = "#1c9099",
"basket_6" = "#67a9cf",
"basket_10" = "#d0d1e6"),
shape_vert = c("basket_1" = 21,
"basket_6" = 22,
"basket_10" = 24),
size_vert = c("basket_1" = 2,
"basket_6" = 2,
"basket_10" = 2),
color_vert = c("basket_1" = "#7a0177",
"basket_6" = "#c51b8a",
"basket_10" = "#fa9fb5"),
fill_vert = c("basket_1" = "#7a0177",
"basket_6" = "#c51b8a",
"basket_10" = "#fa9fb5"))
plot_try
## -----------------------------------------------------------------------------
####### Preliminary steps:
## Compute the range of functional axes:
range_sp_coord <- range(sp_faxes_coord_fruits)
## Based on the range of species coordinates values, compute a nice range ...
## ... for functional axes:
range_faxes <- range_sp_coord +
c(-1, 1) * (range_sp_coord[2] - range_sp_coord[1]) * 0.05
####### Create a list that will contains plots for each combination of axis:
plot_FRic <- list()
####### Compute all the combiantion we can get and the number of plots
axes_plot <- utils::combn(c("PC1", "PC2", "PC3", "PC4"), 2)
plot_nb <- ncol(axes_plot)
######## Loop on all pairs of axes:
# for each combinaison of two axis:
for (k in (1:plot_nb)) {
# get names of axes to plot:
xy_k <- axes_plot[1:2, k]
####### Steps previously showed
# a - Background:
# get species coordinates along the two studied axes:
sp_faxes_coord_xy <- sp_faxes_coord_fruits[, xy_k]
# Plot background with grey backrgound:
plot_k <- mFD::background.plot(range_faxes = range_faxes,
faxes_nm = c(xy_k[1], xy_k[2]),
color_bg = "grey95")
# b - Global convex-hull:
# Retrieve vertices coordinates along the two studied functional axes:
vert <- mFD::vertices(sp_faxes_coord = sp_faxes_coord_xy,
order_2D = FALSE,
check_input = TRUE)
plot_k <- mFD::pool.plot(ggplot_bg = plot_k,
sp_coord2D = sp_faxes_coord_xy,
vertices_nD = vert,
plot_pool = FALSE,
color_pool = NA,
fill_pool = NA,
alpha_ch = 0.8,
color_ch = "white",
fill_ch = "white",
shape_pool = NA,
size_pool = NA,
shape_vert = NA,
size_vert = NA,
color_vert = NA,
fill_vert = NA)
# c - Assemblages convex-hulls and species:
# Step 1: Species coordinates:
# basket_1:
## filter species from basket_1:
sp_filter_basket1 <- mFD::sp.filter(asb_nm = c("basket_1"),
sp_faxes_coord = sp_faxes_coord_xy,
asb_sp_w = baskets_fruits_weights)
## get species coordinates (basket_1):
sp_faxes_coord_basket1 <- sp_filter_basket1$`species coordinates`
# basket_6:
## filter species from basket_6:
sp_filter_basket6 <- mFD::sp.filter(asb_nm = c("basket_6"),
sp_faxes_coord = sp_faxes_coord_xy,
asb_sp_w = baskets_fruits_weights)
## get species coordinates (basket_6):
sp_faxes_coord_basket6 <- sp_filter_basket6$`species coordinates`
# basket_10:
## filter species from basket_10:
sp_filter_basket10 <- mFD::sp.filter(asb_nm = c("basket_10"),
sp_faxes_coord = sp_faxes_coord_xy,
asb_sp_w = baskets_fruits_weights)
## get species coordinates (basket_10):
sp_faxes_coord_basket10 <- sp_filter_basket10$`species coordinates`
# Step 1 follow-up Vertices names:
# basket_1:
vert_nm_basket1 <- mFD::vertices(sp_faxes_coord = sp_faxes_coord_basket1,
order_2D = TRUE,
check_input = TRUE)
# basket_6:
vert_nm_basket6 <- mFD::vertices(sp_faxes_coord = sp_faxes_coord_basket6,
order_2D = TRUE,
check_input = TRUE)
# basket_10:
vert_nm_basket10 <- mFD::vertices(sp_faxes_coord = sp_faxes_coord_basket10,
order_2D = TRUE,
check_input = TRUE)
# Step 2: plot convex-hulls and species of studied assemblages:
plot_k <- mFD::fric.plot(ggplot_bg = plot_k,
asb_sp_coord2D = list("basket_1" = sp_faxes_coord_basket1,
"basket_6" = sp_faxes_coord_basket6,
"basket_10" = sp_faxes_coord_basket10),
asb_vertices_nD = list("basket_1" = vert_nm_basket1,
"basket_6" = vert_nm_basket6,
"basket_10" = vert_nm_basket10),
plot_sp = TRUE,
color_ch = NA,
fill_ch = c("basket_1" = "#1c9099",
"basket_6" = "#67a9cf",
"basket_10" = "#d0d1e6"),
alpha_ch = c("basket_1" = 0.4,
"basket_6" = 0.4,
"basket_10" = 0.4),
shape_sp = c("basket_1" = 21,
"basket_6" = 22,
"basket_10" = 24),
size_sp = c("basket_1" = 2,
"basket_6" = 2,
"basket_10" = 2),
color_sp = c("basket_1" = "#1c9099",
"basket_6" = "#67a9cf",
"basket_10" = "#d0d1e6"),
fill_sp = c("basket_1" = "#1c9099",
"basket_6" = "#67a9cf",
"basket_10" = "#d0d1e6"),
shape_vert = c("basket_1" = 21,
"basket_6" = 22,
"basket_10" = 24),
size_vert = c("basket_1" = 2,
"basket_6" = 2,
"basket_10" = 2),
color_vert = c("basket_1" = "#1c9099",
"basket_6" = "#67a9cf",
"basket_10" = "#d0d1e6"),
fill_vert = c("basket_1" = "#1c9099",
"basket_6" = "#67a9cf",
"basket_10" = "#d0d1e6"))
####### Save the plot on the plot list:
plot_FRic[[k]] <- plot_k
}
## ----fig.height = 3, fig.width = 5, fig.align = "center"----------------------
plot_FRic
## ----fig.height = 6, fig.width = 8, fig.align = "center"----------------------
patchwork_FRic <- (plot_FRic[[1]] + patchwork::plot_spacer() + patchwork::plot_spacer() +
plot_FRic[[2]] + plot_FRic[[4]] + patchwork::plot_spacer() +
plot_FRic[[3]] + plot_FRic[[5]] + plot_FRic[[6]]) +
patchwork::plot_layout(byrow = TRUE, heights = rep(1, 3),
widths = rep(1, 3), ncol = 3, nrow = 3,
guides = "collect")
patchwork_FRic
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## -----------------------------------------------------------------------------
# Load data:
data("baskets_fruits_weights", package = "mFD")
# Display the table:
knitr::kable(as.data.frame(baskets_fruits_weights[1:6, 1:6]),
centering = TRUE,
caption = "Species x assemblages matrix based on the **fruits** dataset")
## -----------------------------------------------------------------------------
# Load data:
data("fruits_traits", package = "mFD")
# Remove fuzzy traits in this tutorial:
fruits_traits <- fruits_traits[ , -c(6:8)]
# Display the table:
knitr::kable(head(fruits_traits),
caption = "Species x traits data frame")
## -----------------------------------------------------------------------------
# Load data:
data("fruits_traits_cat", package = "mFD")
# Remove fuzzy traits in this tutorial:
fruits_traits_cat <- fruits_traits_cat[-c(6:8), ]
# Thus remove the "fuzzy_name" column:
fruits_traits_cat <- fruits_traits_cat[ , -3]
# Display the table:
knitr::kable(head(fruits_traits_cat),
caption = "Traits types based on **fruits & baskets** dataset")
## ----results = "hide"---------------------------------------------------------
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)
## ----results = "hide", message = FALSE----------------------------------------
# Quality of functional spaces:
fspaces_quality_fruits <- mFD::quality.fspaces(
sp_dist = sp_dist_fruits,
maxdim_pcoa = 10,
deviation_weighting = "absolute",
fdist_scaling = FALSE,
fdendro = "average")
# retrieve species (fruits) coordinates in the 4D space (see General tutorial):
sp_faxes_coord_fruits <- fspaces_quality_fruits$"details_fspaces"$"sp_pc_coord"
## ----results = "hide", message = FALSE----------------------------------------
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)
## -----------------------------------------------------------------------------
# Compute the range of functional axes:
range_sp_coord <- range(sp_faxes_coord_fruits)
# Based on the range of species coordinates values, compute a nice range ...
# ... for functional axes:
range_faxes <- range_sp_coord +
c(-1, 1) * (range_sp_coord[2] - range_sp_coord[1]) * 0.05
range_faxes
## ----fig.height = 3, fig.width = 5, fig.align = "center"----------------------
# get species coordinates along the two studied axes:
sp_faxes_coord_xy <- sp_faxes_coord_fruits[, c("PC1", "PC2")]
# Plot background with grey backrgound:
plot_k <- mFD::background.plot(range_faxes = range_faxes,
faxes_nm = c("PC1", "PC2"),
color_bg = "grey95")
plot_k
## -----------------------------------------------------------------------------
# Retrieve vertices coordinates along the two studied functional axes:
vert <- mFD::vertices(sp_faxes_coord = sp_faxes_coord_xy,
order_2D = FALSE,
check_input = TRUE)
## ----fig.height = 3, fig.width = 5, fig.align = "center"----------------------
plot_sp_vert <- mFD::pool.plot(ggplot_bg = plot_k,
sp_coord2D = sp_faxes_coord_xy,
vertices_nD = vert,
plot_pool = TRUE,
color_pool = "black",
fill_pool = NA,
alpha_ch = 0.8,
color_ch = NA,
fill_ch = "white",
shape_pool = 3,
size_pool = 0.8,
shape_vert = 16,
size_vert = 1,
color_vert = "green",
fill_vert = "green")
plot_sp_vert
## ----fig.height = 3, fig.width = 5, fig.align = "center"----------------------
plot_k <- mFD::pool.plot(ggplot_bg = plot_k,
sp_coord2D = sp_faxes_coord_xy,
vertices_nD = vert,
plot_pool = FALSE,
color_pool = NA,
fill_pool = NA,
alpha_ch = 0.8,
color_ch = "white",
fill_ch = "white",
shape_pool = NA,
size_pool = NA,
shape_vert = NA,
size_vert = NA,
color_vert = NA,
fill_vert = NA)
plot_k
## -----------------------------------------------------------------------------
# basket_1:
## filter species from basket_1:
sp_filter_basket1 <- mFD::sp.filter(asb_nm = c("basket_1"),
sp_faxes_coord = sp_faxes_coord_xy,
asb_sp_w = baskets_fruits_weights)
## get species coordinates (basket_1):
sp_faxes_coord_basket1 <- sp_filter_basket1$`species coordinates`
# basket_6:
## filter species from basket_6:
sp_filter_basket6 <- mFD::sp.filter(asb_nm = c("basket_6"),
sp_faxes_coord = sp_faxes_coord_xy,
asb_sp_w = baskets_fruits_weights)
## get species coordinates (basket_6):
sp_faxes_coord_basket6 <- sp_filter_basket6$`species coordinates`
# basket_10:
## filter species from basket_10:
sp_filter_basket10 <- mFD::sp.filter(asb_nm = c("basket_10"),
sp_faxes_coord = sp_faxes_coord_xy,
asb_sp_w = baskets_fruits_weights)
## get species coordinates (basket_10):
sp_faxes_coord_basket10 <- sp_filter_basket10$`species coordinates`
## -----------------------------------------------------------------------------
sp_faxes_coord_basket1
## -----------------------------------------------------------------------------
# basket_1:
vert_nm_basket1 <- mFD::vertices(sp_faxes_coord = sp_faxes_coord_basket1,
order_2D = TRUE,
check_input = TRUE)
# basket_6:
vert_nm_basket6 <- mFD::vertices(sp_faxes_coord = sp_faxes_coord_basket6,
order_2D = TRUE,
check_input = TRUE)
# basket_10:
vert_nm_basket10 <- mFD::vertices(sp_faxes_coord = sp_faxes_coord_basket10,
order_2D = TRUE,
check_input = TRUE)
## ----fig.height = 3, fig.width = 5, fig.align = "center"----------------------
plot_try <- mFD::fric.plot(ggplot_bg = plot_k,
asb_sp_coord2D = list("basket_1" = sp_faxes_coord_basket1,
"basket_6" = sp_faxes_coord_basket6,
"basket_10" = sp_faxes_coord_basket10),
asb_vertices_nD = list("basket_1" = vert_nm_basket1,
"basket_6" = vert_nm_basket6,
"basket_10" = vert_nm_basket10),
plot_sp = FALSE,
color_ch = NA,
fill_ch = c("basket_1" = "#1c9099",
"basket_6" = "#67a9cf",
"basket_10" = "#d0d1e6"),
alpha_ch = c("basket_1" = 0.4,
"basket_6" = 0.4,
"basket_10" = 0.4),
shape_sp = NA,
size_sp = NA,
color_sp = NA,
fill_sp = NA,
shape_vert = NA,
size_vert = NA,
color_vert = NA,
fill_vert = NA)
plot_try
## ----fig.height = 3, fig.width = 5, fig.align = "center"----------------------
plot_try <- mFD::fric.plot(ggplot_bg = plot_k,
asb_sp_coord2D = list("basket_1" = sp_faxes_coord_basket1,
"basket_6" = sp_faxes_coord_basket6,
"basket_10" = sp_faxes_coord_basket10),
asb_vertices_nD = list("basket_1" = vert_nm_basket1,
"basket_6" = vert_nm_basket6,
"basket_10" = vert_nm_basket10),
plot_sp = FALSE,
color_ch = c("basket_1" = "#7a0177",
"basket_6" = "#c51b8a",
"basket_10" = "#fa9fb5"),
fill_ch = c("basket_1" = "#1c9099",
"basket_6" = "#67a9cf",
"basket_10" = "#d0d1e6"),
alpha_ch = c("basket_1" = 0.4,
"basket_6" = 0.4,
"basket_10" = 0.4),
shape_sp = NA,
size_sp = NA,
color_sp = NA,
fill_sp = NA,
shape_vert = NA,
size_vert = NA,
color_vert = NA,
fill_vert = NA)
plot_try
## ----fig.height = 3, fig.width = 5, fig.align = "center"----------------------
plot_try <- mFD::fric.plot(ggplot_bg = plot_k,
asb_sp_coord2D = list("basket_1" = sp_faxes_coord_basket1,
"basket_6" = sp_faxes_coord_basket6,
"basket_10" = sp_faxes_coord_basket10),
asb_vertices_nD = list("basket_1" = vert_nm_basket1,
"basket_6" = vert_nm_basket6,
"basket_10" = vert_nm_basket10),
plot_sp = TRUE,
color_ch = NA,
fill_ch = c("basket_1" = "#1c9099",
"basket_6" = "#67a9cf",
"basket_10" = "#d0d1e6"),
alpha_ch = c("basket_1" = 0.4,
"basket_6" = 0.4,
"basket_10" = 0.4),
shape_sp = c("basket_1" = 21,
"basket_6" = 22,
"basket_10" = 24),
size_sp = c("basket_1" = 2,
"basket_6" = 2,
"basket_10" = 2),
color_sp = c("basket_1" = "#1c9099",
"basket_6" = "#67a9cf",
"basket_10" = "#d0d1e6"),
fill_sp = c("basket_1" = "#1c9099",
"basket_6" = "#67a9cf",
"basket_10" = "#d0d1e6"),
shape_vert = c("basket_1" = 21,
"basket_6" = 22,
"basket_10" = 24),
size_vert = c("basket_1" = 2,
"basket_6" = 2,
"basket_10" = 2),
color_vert = c("basket_1" = "#1c9099",
"basket_6" = "#67a9cf",
"basket_10" = "#d0d1e6"),
fill_vert = c("basket_1" = "#1c9099",
"basket_6" = "#67a9cf",
"basket_10" = "#d0d1e6"))
plot_try
## ----fig.height = 3, fig.width = 5, fig.align = "center"----------------------
plot_try <- mFD::fric.plot(ggplot_bg = plot_k,
asb_sp_coord2D = list("basket_1" = sp_faxes_coord_basket1,
"basket_6" = sp_faxes_coord_basket6,
"basket_10" = sp_faxes_coord_basket10),
asb_vertices_nD = list("basket_1" = vert_nm_basket1,
"basket_6" = vert_nm_basket6,
"basket_10" = vert_nm_basket10),
plot_sp = TRUE,
color_ch = NA,
fill_ch = c("basket_1" = "#1c9099",
"basket_6" = "#67a9cf",
"basket_10" = "#d0d1e6"),
alpha_ch = c("basket_1" = 0.4,
"basket_6" = 0.4,
"basket_10" = 0.4),
shape_sp = c("basket_1" = 21,
"basket_6" = 22,
"basket_10" = 24),
size_sp = c("basket_1" = 2,
"basket_6" = 2,
"basket_10" = 2),
color_sp = c("basket_1" = "#1c9099",
"basket_6" = "#67a9cf",
"basket_10" = "#d0d1e6"),
fill_sp = c("basket_1" = "#1c9099",
"basket_6" = "#67a9cf",
"basket_10" = "#d0d1e6"),
shape_vert = c("basket_1" = 21,
"basket_6" = 22,
"basket_10" = 24),
size_vert = c("basket_1" = 2,
"basket_6" = 2,
"basket_10" = 2),
color_vert = c("basket_1" = "#7a0177",
"basket_6" = "#c51b8a",
"basket_10" = "#fa9fb5"),
fill_vert = c("basket_1" = "#7a0177",
"basket_6" = "#c51b8a",
"basket_10" = "#fa9fb5"))
plot_try
## -----------------------------------------------------------------------------
####### Preliminary steps:
## Compute the range of functional axes:
range_sp_coord <- range(sp_faxes_coord_fruits)
## Based on the range of species coordinates values, compute a nice range ...
## ... for functional axes:
range_faxes <- range_sp_coord +
c(-1, 1) * (range_sp_coord[2] - range_sp_coord[1]) * 0.05
####### Create a list that will contains plots for each combination of axis:
plot_FRic <- list()
####### Compute all the combiantion we can get and the number of plots
axes_plot <- utils::combn(c("PC1", "PC2", "PC3", "PC4"), 2)
plot_nb <- ncol(axes_plot)
######## Loop on all pairs of axes:
# for each combinaison of two axis:
for (k in (1:plot_nb)) {
# get names of axes to plot:
xy_k <- axes_plot[1:2, k]
####### Steps previously showed
# a - Background:
# get species coordinates along the two studied axes:
sp_faxes_coord_xy <- sp_faxes_coord_fruits[, xy_k]
# Plot background with grey backrgound:
plot_k <- mFD::background.plot(range_faxes = range_faxes,
faxes_nm = c(xy_k[1], xy_k[2]),
color_bg = "grey95")
# b - Global convex-hull:
# Retrieve vertices coordinates along the two studied functional axes:
vert <- mFD::vertices(sp_faxes_coord = sp_faxes_coord_xy,
order_2D = FALSE,
check_input = TRUE)
plot_k <- mFD::pool.plot(ggplot_bg = plot_k,
sp_coord2D = sp_faxes_coord_xy,
vertices_nD = vert,
plot_pool = FALSE,
color_pool = NA,
fill_pool = NA,
alpha_ch = 0.8,
color_ch = "white",
fill_ch = "white",
shape_pool = NA,
size_pool = NA,
shape_vert = NA,
size_vert = NA,
color_vert = NA,
fill_vert = NA)
# c - Assemblages convex-hulls and species:
# Step 1: Species coordinates:
# basket_1:
## filter species from basket_1:
sp_filter_basket1 <- mFD::sp.filter(asb_nm = c("basket_1"),
sp_faxes_coord = sp_faxes_coord_xy,
asb_sp_w = baskets_fruits_weights)
## get species coordinates (basket_1):
sp_faxes_coord_basket1 <- sp_filter_basket1$`species coordinates`
# basket_6:
## filter species from basket_6:
sp_filter_basket6 <- mFD::sp.filter(asb_nm = c("basket_6"),
sp_faxes_coord = sp_faxes_coord_xy,
asb_sp_w = baskets_fruits_weights)
## get species coordinates (basket_6):
sp_faxes_coord_basket6 <- sp_filter_basket6$`species coordinates`
# basket_10:
## filter species from basket_10:
sp_filter_basket10 <- mFD::sp.filter(asb_nm = c("basket_10"),
sp_faxes_coord = sp_faxes_coord_xy,
asb_sp_w = baskets_fruits_weights)
## get species coordinates (basket_10):
sp_faxes_coord_basket10 <- sp_filter_basket10$`species coordinates`
# Step 1 follow-up Vertices names:
# basket_1:
vert_nm_basket1 <- mFD::vertices(sp_faxes_coord = sp_faxes_coord_basket1,
order_2D = TRUE,
check_input = TRUE)
# basket_6:
vert_nm_basket6 <- mFD::vertices(sp_faxes_coord = sp_faxes_coord_basket6,
order_2D = TRUE,
check_input = TRUE)
# basket_10:
vert_nm_basket10 <- mFD::vertices(sp_faxes_coord = sp_faxes_coord_basket10,
order_2D = TRUE,
check_input = TRUE)
# Step 2: plot convex-hulls and species of studied assemblages:
plot_k <- mFD::fric.plot(ggplot_bg = plot_k,
asb_sp_coord2D = list("basket_1" = sp_faxes_coord_basket1,
"basket_6" = sp_faxes_coord_basket6,
"basket_10" = sp_faxes_coord_basket10),
asb_vertices_nD = list("basket_1" = vert_nm_basket1,
"basket_6" = vert_nm_basket6,
"basket_10" = vert_nm_basket10),
plot_sp = TRUE,
color_ch = NA,
fill_ch = c("basket_1" = "#1c9099",
"basket_6" = "#67a9cf",
"basket_10" = "#d0d1e6"),
alpha_ch = c("basket_1" = 0.4,
"basket_6" = 0.4,
"basket_10" = 0.4),
shape_sp = c("basket_1" = 21,
"basket_6" = 22,
"basket_10" = 24),
size_sp = c("basket_1" = 2,
"basket_6" = 2,
"basket_10" = 2),
color_sp = c("basket_1" = "#1c9099",
"basket_6" = "#67a9cf",
"basket_10" = "#d0d1e6"),
fill_sp = c("basket_1" = "#1c9099",
"basket_6" = "#67a9cf",
"basket_10" = "#d0d1e6"),
shape_vert = c("basket_1" = 21,
"basket_6" = 22,
"basket_10" = 24),
size_vert = c("basket_1" = 2,
"basket_6" = 2,
"basket_10" = 2),
color_vert = c("basket_1" = "#1c9099",
"basket_6" = "#67a9cf",
"basket_10" = "#d0d1e6"),
fill_vert = c("basket_1" = "#1c9099",
"basket_6" = "#67a9cf",
"basket_10" = "#d0d1e6"))
####### Save the plot on the plot list:
plot_FRic[[k]] <- plot_k
}
## ----fig.height = 3, fig.width = 5, fig.align = "center"----------------------
plot_FRic
## ----fig.height = 6, fig.width = 8, fig.align = "center"----------------------
patchwork_FRic <- (plot_FRic[[1]] + patchwork::plot_spacer() + patchwork::plot_spacer() +
plot_FRic[[2]] + plot_FRic[[4]] + patchwork::plot_spacer() +
plot_FRic[[3]] + plot_FRic[[5]] + plot_FRic[[6]]) +
patchwork::plot_layout(byrow = TRUE, heights = rep(1, 3),
widths = rep(1, 3), ncol = 3, nrow = 3,
guides = "collect")
patchwork_FRic
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