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Plot functional space and chosen functional indices

Source: R/plot_alpha_indices.R
alpha.multidim.plot.Rd

Compute a graphical representation of functional indices. To plot functional indices, functional indices values must have been retrieve through the use of the alpha.fd.multidim function.

Usage

alpha.multidim.plot(
  output_alpha_fd_multidim,
  plot_asb_nm,
  ind_nm = c("fide", "fric", "fdiv", "fdis", "feve", "fori", "fspe", "fnnd"),
  faxes = NULL,
  faxes_nm = NULL,
  range_faxes = c(NA, NA),
  color_bg = "grey95",
  shape_sp = c(pool = 3, asb1 = 21, asb2 = 21),
  size_sp = c(pool = 0.7, asb1 = 1, asb2 = 1),
  color_sp = c(pool = "grey50", asb1 = "#0072B2", asb2 = "#D55E00"),
  color_vert = c(pool = "grey50", asb1 = "#0072B2", asb2 = "#D55E00"),
  fill_sp = c(pool = NA, asb1 = "#FFFFFF30", asb2 = "#FFFFFF30"),
  fill_vert = c(pool = NA, asb1 = "#0072B2", asb2 = "#D55E00"),
  color_ch = c(pool = NA, asb1 = "#0072B2", asb2 = "#D55E00"),
  fill_ch = c(pool = "white", asb1 = "#0072B2", asb2 = "#D55E00"),
  alpha_ch = c(pool = 1, asb1 = 0.3, asb2 = 0.3),
  shape_centroid_fdis = c(asb1 = 22, asb2 = 22),
  shape_centroid_fdiv = c(asb1 = 24, asb2 = 25),
  shape_centroid_fspe = 23,
  color_centroid_fspe = "black",
  size_sp_nm = 3,
  color_sp_nm = "black",
  plot_sp_nm = NULL,
  fontface_sp_nm = "plain",
  save_file = FALSE,
  check_input = TRUE
)

Arguments

output_alpha_fd_multidim

a list of objects retrieved through the alpha.fd.multidim function.

plot_asb_nm

a vector containing name(s) of assemblage(s) to plot.

ind_nm

a vector of character string of the name of functional indices to plot. Indices names must be written in lower case letters. Possible indices to compute are: "fdis", "feve", "fric", "fdiv", "fori" and "fspe". Default: all the indices are computed.

faxes

a vector with names of axes to plot. You can only plot from 2 to 4 axes for graphical reasons: vector length should be between 2 and 4. Default: faxes = NULL (the four first axes will be plotted).

faxes_nm

a vector with axes labels if the user want different axes labels than faxes ones. Default: faxes_nm = faxes (labels will the the same that faxes ones).

range_faxes

a vector with minimum and maximum for values for axes. Note that to have a fair representation of position of species in all plots, all axes must have the same range. Default: faxes_lim = c(NA, NA) (the range is computed according to the range of values among all axes, all axes having the same range).

color_bg

a R color name or an hexadecimal code used to fill plot background. Default: color_bg = "grey95".

shape_sp

a vector gathering numeric values referring to the symbol used to draw species from the global pool and the plotted assemblage(s). It should be written as c(pool = "...", asb1 = "...", ...). (0 = high transparency, 1 = no transparency).

size_sp

a vector gathering numeric values referring to the size of species belonging to the global pool and the plotted assemblage(s). It should be written as c(pool = "...", asb1 = "...", ...).

color_sp

a vector gathering R color names or hexadecimal codes referring to the color of species from the global pool and studied assemblage(s). It should be written as c(pool = "...", asb1 = "...", ...).

color_vert

a vector gathering R color names or hexadecimal codes referring to the color of vertices from the global pool and studied assemblage(s). It should be written as c(pool = "...", asb1 = "...", ...).

fill_sp

a vector gathering R color names or hexadecimal codes referring to the filled color of species from the global pool and studied assemblage(s). It should be written as c(pool = "...", asb1 = "...", ...).

fill_vert

a vector gathering R color names or hexadecimal codes referring to the filled color of vertices from the global pool and studied assemblage(s). It should be written as c(pool = "...", asb1 = "...", ...).

color_ch

a vector gathering R color names or hexadecimal codes referring to the color of the convex pool of the global pool and studied assemblage(s). It should be written as c(pool = "...", asb1 = "...", ...).

fill_ch

a vector gathering R color names or hexadecimal codes referring to the color to fill the convex pool of the global pool and studied assemblage(s). It should be written as c(pool = "...", asb1 = "...", ...).

alpha_ch

a vector gathering numeric values referring to the opacity of convex hulls of the global pool and the plotted assemblage(s). It should be written as c(pool = "...", asb1 = "...", ...). (0 = high transparency, 1 = no transparency).

shape_centroid_fdis

a vector gathering numeric value(s) used to draw FDis centroid size.

shape_centroid_fdiv

a vector gathering numeric value(s) used to draw FDiv centroid size.

shape_centroid_fspe

a vector gathering numeric value used to draw FSpe centroid (i.e. center of the functional space) size.

color_centroid_fspe

a vector gathering R color name or hexadecimal code used to draw FSpe centroid (i.e. center of the functional space) color.

size_sp_nm

a numeric value referring to the size of species names if plotted.

color_sp_nm

a R color name or hexadecimal code referring to the color of names of species if plotted.

plot_sp_nm

a vector containing species names that are to be plotted. Default: plot_nm_sp = NULL (no name plotted).

fontface_sp_nm

a character string for font of species labels (e.g. "italic", "bold"). Default: fontface_sp_nm = 'plain'.

save_file

a logical value telling if plots should be locally saved or not.

check_input

a logical value indicating whether key features the inputs are checked (e.g. class and/or mode of objects, names of rows and/or columns, missing values). If an error is detected, a detailed message is returned. Default: check.input = TRUE.

Value

If name_file is NULL, it returns a list of one ggplot2 plots per functional index containing plots for combinations of up to four axes, a patchwork figure gathering all combinations of axes and a ggplot2 figure showing the plot caption. If name_file is not NULL, then those plots are saved locally.

Author

Camille Magneville and Sebastien Villeger

Examples

# \donttest{

# 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

# Compute alpha diversity indices:
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("fdis", "fmpd", "fnnd", "feve", "fric", "fdiv",
                       "fori", "fspe"),
  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%

# Plot all fd alpha indices:
plots_alpha <- mFD::alpha.multidim.plot(
output_alpha_fd_multidim = alpha_fd_indices_fruits,
plot_asb_nm              = c("basket_1", "basket_5"),
ind_nm                   = c("fdis", "fide", "fnnd", "feve", 
                             "fric", "fdiv", "fori", 
                             "fspe"),
faxes                    = NULL,
faxes_nm                 = NULL,
range_faxes              = c(NA, NA),
color_bg                 = "grey95",
shape_sp                 = c(pool = 3, asb1 = 21, 
                             asb2 = 21),
size_sp                  = c(pool = 0.7, asb1 = 1, 
                             asb2 = 1),
color_sp                 = c(pool = "grey50", 
                             asb1 = "#1F968BFF",
                             asb2 = "#DCE319FF"),
color_vert               = c(pool = "grey50", 
                             asb1 = "#1F968BFF",
                             asb2 = "#DCE319FF"),
fill_sp                 = c(pool =  NA, 
                            asb1 = "#1F968BFF",
                            asb2 = "#DCE319FF"),
fill_vert               = c(pool = NA, 
                            asb1 = "#1F968BFF",
                            asb2 = "#DCE319FF"),
color_ch                = c(pool = NA, 
                            asb1 = "#1F968BFF",
                            asb2 = "#DCE319FF"),
fill_ch                 = c(pool = "white", 
                            asb1 = "#1F968BFF",
                            asb2 = "#DCE319FF"),
alpha_ch                = c(pool = 1, asb1 = 0.3, 
                            asb2 = 0.3),
shape_centroid_fdis     = c(asb1 = 22,  asb2 = 24),
shape_centroid_fdiv     = c(asb1 = 22,  asb2 = 24),
shape_centroid_fspe     = 23,
color_centroid_fspe     = "black",
size_sp_nm              = 3, 
color_sp_nm             = "black",
plot_sp_nm              = NULL,
fontface_sp_nm          = "plain",
save_file               = FALSE,
check_input             = TRUE) 

# Check FRic plot:
plots_alpha$fric$patchwork

# }