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This plot fDiv indice for a given pair of functional axes and one or several assemblages. This function adds mean distance to center of gravity of vertices, points and vertices of 1:N assemblages on the background plot

Usage

fdiv.plot(
  ggplot_bg,
  asb_sp_coord2D,
  asb_sp_relatw,
  asb_vertices_nD,
  asb_vertG_coord2D,
  plot_sp = TRUE,
  shape_sp,
  color_sp,
  fill_sp,
  shape_vert,
  color_vert,
  fill_vert,
  shape_vertG,
  size_vertG,
  color_vertG,
  fill_vertG
)

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 functional axes.

asb_sp_relatw

a list of vector gathering species relative weight in each assemblage. It can be retrieved through the alpha.fd.multidim.

asb_vertices_nD

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

asb_vertG_coord2D

a list (with names as in asb_sp_coord2D) containing for each assemblage the coordinates of center of gravity of vertices for a given pair of axes

plot_sp

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

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", ...).

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", ...).

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

shape_vertG

a numeric value referring to the shape to use to plot the center of gravity of vertices 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_vertG

a numeric value referring to the size of the symbol used for the center of gravity of vertices 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_vertG

a R color name or an hexadecimal code referring to the color of the center of gravity 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", ...).

fill_vertG

a R color name or an hexadecimal code referring to the color to fill the center of gravity of vertices (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", ...).

Value

A ggplot object plotting background of multidimensional graphs and FDiv indice.

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

# 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 the matrix of species coordinates for "basket_1" and PC1 and PC2
 sp_filter <- mFD::sp.filter(asb_nm          = "basket_1", 
                             sp_faxes_coord = sp_faxes_coord_fruits, 
                             asb_sp_w       = baskets_fruits_weights)
 fruits_asb_sp_coord_b1 <- sp_filter$`species coordinates`
 fruits_asb_sp_coord2D_b1 <- fruits_asb_sp_coord_b1[, c("PC1", "PC2")]
                               
 # Use alpha.fd.multidim() function to get inputs to plot FDiv:
 alpha_fd_ind <- 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("fdiv"),
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%
  
 # Retrieve inputs of the fdiv.plot() function for "basket_1" and PC1, PC2
 # ... through alpha.fd.multidim outputs:
 fruits_asb_sp_relatw_b1 <- 
         alpha_fd_ind$details$asb_sp_relatw["basket_1", ]
 fruits_asb_vertices_nD_b1_2D <- 
                     alpha_fd_ind$details$asb_vert_nm["basket_1"]
 fruits_asb_vertG_coord_b1 <- 
                     alpha_fd_ind$details$asb_G_coord["basket_1"]
 fruits_asb_vertG_coord_b1_2D <- 
             fruits_asb_vertG_coord_b1[[1]][c("PC1", "PC2")]
 
 # Retrieve FDiv plot:
 fdiv_plot <- fdiv.plot(
           ggplot_bg         = ggplot_bg_fruits,
           asb_sp_coord2D    = list(basket_1 = fruits_asb_sp_coord2D_b1),
           asb_sp_relatw     = list(basket_1 = fruits_asb_sp_relatw_b1),
           asb_vertices_nD   = fruits_asb_vertices_nD_b1_2D,
           asb_vertG_coord2D = list(basket_1 = fruits_asb_vertG_coord_b1_2D),
           plot_sp           = TRUE,
           shape_sp          = 16,
           color_sp          = c(basket_1 = "red"),
           fill_sp           = "red",
           color_vert        = "red",
           fill_vert         = "red",
           shape_vert        = 16,
           shape_vertG       = list(basket_1 = 18),
           size_vertG        = list(basket_1 = 2),
           color_vertG       = list(basket_1 = "blue"),
           fill_vertG        = list(basket_1 = "blue"))
 fdiv_plot