This function plots FRic index for a given pair of functional axes and one or several assemblages. It adds convex hull(s), points and vertices of 1:N assemblages on the background plot

fric.plot(
ggplot_bg,
asb_sp_coord2D,
asb_vertices_nD,
plot_sp = TRUE,
color_ch,
fill_ch,
alpha_ch,
shape_sp,
size_sp,
color_sp,
fill_sp,
shape_vert,
size_vert,
color_vert,
fill_vert
)

## Arguments

ggplot_bg

a ggplot object of the plot background retrieved through the background.plot function.

asb_sp_coord2D

a list of matrix (ncol = 2) with coordinates of species present in each assemblage for a given pair of axes for a given pair of functional axes.

asb_vertices_nD

a list (with names as in asb_sp_coord2D) of vectors with names of species being vertices in n dimensions.

plot_sp

a logical value indicating whether species of each assemblage should be plotted or not. Default: plot_sp = TRUE.

color_ch

a R color name or an hexadecimal code referring to the color of the border of the convex hull filled by the pool of species if one assemblage to plot or a vector of R color names or hexadecimal codes if several assemblages to plot. If more than one assemblage to plot, the vector should be formatted as: c(asb1 = "firstRcolorname", asb2 = "secondRcolorname", ...).

fill_ch

a R color name or an hexadecimal code referring to the color of convex hull filling if one assemblage to plot or a vector of R color names or hexadecimal codes if several assemblages to plot. If more than one assemblage to plot, the vector should be formatted as: c(asb1 = "firstRcolorname", asb2 = "secondRcolorname", ...).

alpha_ch

a numeric value referring to the value of transparency of the convex hull filling (0 = high transparency, 1 = no transparency) if one assemblage to plot or a vector numeric values if several assemblages to plot. If more than one assemblage to plot, the vector should be formatted as: c(asb1 = "firstRtransparency", asb2 = "secondRtransparency", ...).

shape_sp

a numeric value referring to the shape of the symbol used for species plotting if one assemblage to plot or a vector numeric values if several assemblages to plot. If more than one assemblage to plot, the vector should be formatted as: c(asb1 = "firstRshape", asb2 = "secondRshape", ...).

size_sp

a numeric value referring to the size of the symbol used for species plotting if one assemblage to plot or a vector numeric values if several assemblages to plot. If more than one assemblage to plot, the vector should be formatted as: c(asb1 = "firstRsize", asb2 = "secondRsize", ...).

color_sp

a R color name or an hexadecimal code referring to the color of species if one assemblage to plot or a vector of R color names or hexadecimal codes if several assemblages to plot. If more than one assemblage to plot, the vector should be formatted as: c(asb1 = "firstRcolorname", asb2 = "secondRcolorname", ...).

fill_sp

a R color name or an hexadecimal code referring to the color of species symbol filling (if shape_sp > 20) if one assemblage to plot or a vector of R color names or hexadecimal codes if several assemblages to plot. If more than one assemblage to plot, the vector should be formatted as: c(asb1 = "firstRcolorname", asb2 = "secondRcolorname", ...).

shape_vert

a numeric value referring to the shape of the symbol used for vertices plotting if one assemblage to plot or a vector numeric values if several assemblages to plot. If more than one assemblage to plot, the vector should be formatted as: c(asb1 = "firstRshape", asb2 = "secondRshape", ...).

size_vert

a numeric value referring to the size of the symbol used for vertices plotting if one assemblage to plot or a vector numeric values if several assemblages to plot. If more than one assemblage to plot, the vector should be formatted as: c(asb1 = "firstRsize", asb2 = "secondRsize", ...).

color_vert

a R color name or an hexadecimal code referring to the color of vertices if one assemblage to plot or a vector of R color names or hexadecimal codes if several assemblages to plot. If more than one assemblage to plot, the vector should be formatted as: c(asb1 = "firstRcolorname", asb2 = "secondRcolorname", ...). If color_vert = NA, vertices are not plotted (for shapes only defined by color, ie shape inferior to 20. Otherwise fill must also be set to NA).

fill_vert

a R color name or an hexadecimal code referring to the color of vertices symbol filling (if shape_vert >20) if one assemblage to plot or a vector of R color names or hexadecimal codes if several assemblages to plot. If more than one assemblage to plot, the vector should be formatted as: c(asb1 = "firstRcolorname", asb2 = "secondRcolorname", ...). If fill = NA and color = NA, vertices are not plotted (if shape_vert superior to 20

## Value

A ggplot object plotting background of multidimensional graphs and FRic convex hulls.

## Author

Camille Magneville and Sebastien Villeger

## Examples

# 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 studid 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