fide.plot {mFD}

Plot FIde index

Description

Plot FIde index given a pair of functional axes for one or several assemblages. It adds the centroid of species for each assemblage and segments showing centroid coordinates on functional axes on the background plot.

Usage

fide.plot(
  ggplot_bg,
  asb_sp_coord2D,
  asb_sp_relatw,
  asb_fide_coord2D,
  plot_sp = TRUE,
  shape_sp,
  color_sp,
  fill_sp,
  shape_fide,
  size_fide,
  color_fide,
  fill_fide,
  color_segment,
  width_segment,
  linetype_segment
)

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_fide_coord2D

a list (with names as in asb_sp_coord2D) of vectors with coordinates of the centroid of species for each assemblage 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_fide

a numeric value referring to the shape of the symbol used for fide centroid 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_fide

a numeric value referring to the size of the symbol used for fide centroid 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_fide

a R color name or an hexadecimal code referring to the color of species centroid for agiven assemblage 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_fide

a R color name or an hexadecimal code referring to the color to fill assemblage centroid symbol (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", ...).

color_segment

a R color name or an hexadecimal code referring to the color of of the segment linking axes and centroid from the studied assemblage 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", ...).

width_segment

a numeric value referring to the width of the segment linking fide centroid and functional axes 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", ...).

linetype_segment

a numeric value referring to the linetype of the segment linking fide centroid and functional axes 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 = "firstRlinetype", asb2 = "secondRlinetype", ...).

Value

A ggplot object with FIde index, species and background.

Author(s)

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)
  
# 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 FIde:
 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("fide"),
  scaling          = TRUE,
  check_input      = TRUE,
  details_returned = TRUE)
  
 # Retrieve fide values through alpha.fd.multidim outputs:
 fruits_asb_fide_coord2D <- 
  alpha_fd_indices_fruits$functional_diversity_indices[c("fide_PC1", 
                                                         "fide_PC2")]
 fruits_asb_fide_coord2D_b1 <- fruits_asb_fide_coord2D[c("basket_1"), ]
 fruits_asb_sp_relatw_b1 <- 
         alpha_fd_indices_fruits$details$asb_sp_relatw["basket_1", ]
 
 # Retrieve FIde plot:
 fide_plot <- fide.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_fide_coord2D = list(basket_1 = fruits_asb_fide_coord2D_b1),
           plot_sp = TRUE,
           shape_sp = 16,
           color_sp = "red",
           fill_sp = "red",
           shape_fide = list(basket_1 = 18),
           size_fide = list(basket_1 = 5),
           color_fide = list(basket_1 = "blue"),
           fill_fide = list(basket_1 = "blue"),
           color_segment = list(basket_1 = "red"),
           width_segment = list(basket_1 = 1),
           linetype_segment = list(basket_1 = "dashed"))
           
 fide_plot