| fori.plot {mFD} | R Documentation |
Plot FOri
Description
This function plots FOri index for a given pair of functional axes and for one or several assemblages. It adds the distance of species from the studied to their nearest neighbour(s) from the global pool.
Usage
fori.plot(
ggplot_bg,
asb_sp_coord2D,
asb_sp_relatw,
asb_nn_pool,
pool_coord2D,
plot_pool = TRUE,
plot_sp = TRUE,
shape_pool,
size_pool,
color_pool,
fill_pool,
shape_sp,
color_sp,
fill_sp,
color_segment,
width_segment,
linetype_segment
)
Arguments
ggplot_bg |
a ggplot object of the plot background retrieved through
the |
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
|
asb_nn_pool |
a list gathering for each species of a studied assemblage its nearest neighbour(s) in the global pool. |
pool_coord2D |
a matrix (ncol = 2) with coordinates of species present in the global pool for a given pair of functional axes. |
plot_pool |
a logical value indicating whether species of each
assemblage should be plotted or not. Default: |
plot_sp |
a logical value indicating whether species of each assemblage
should be plotted or not. Default: |
shape_pool |
a numeric value referring to the shape used to plot species pool. |
size_pool |
a numeric value referring to the size of species belonging to the global pool. |
color_pool |
a R color name or an hexadecimal code referring to the color of the pool. This color is also used for FRic convex hull color. |
fill_pool |
a R color name or an hexadecimal code referring to the
colour to fill species symbol (if |
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 |
color_segment |
color_segment a R color name or an hexadecimal code referring to the color of of the segment linking nearest neighbors in the global pool 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 size of the segment linking nearest neighbors in the global pool or a vector of numeric values if several assemblages to plot. If more than one assemblage to plot, the vector should be formatted as: c(asb1 = "firstRwidth", asb2 = "secondRwidth", ...). |
linetype_segment |
a character string referring to the linetype used to link nearest neighbors in the global pool or a vector of character strings 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 FOri index.
Author(s)
Camille Magneville and Sebastien Villeger
Examples
## Not run:
# 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$`species coordinates`
fruits_asb_sp_coord2D_b1 <- fruits_asb_sp_coord_b1[, c("PC1", "PC2")]
# Use alpha.fd.multidim() function to get inputs to plot FIde:
alpha_fd_indices_fruits <- mFD::alpha.fd.multidim(
sp_faxes_coord = sp_faxes_coord_fruits[, c("PC1", "PC2", "PC3", "PC4")],
asb_sp_w = baskets_fruits_weights,
ind_vect = c("fori"),
scaling = TRUE,
check_input = TRUE,
details_returned = TRUE)
# Retrieve nearest neighbor(s) names through alpha.fd.multidim outputs:
fruits_asb_nn_pool_b1 <-
alpha_fd_indices_fruits$details$asb_nm_nn_pool["basket_1"]
# Retrieve FNND plot:
fori_plot <- fori.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_nn_pool = fruits_asb_nn_pool_b1,
pool_coord2D = sp_faxes_coord_fruits[, c("PC1", "PC2")],
plot_pool = TRUE,
plot_sp = TRUE,
shape_sp = 16,
color_sp = "red",
fill_sp = "red",
shape_pool = 4,
size_pool = 2,
color_pool = "grey",
fill_pool = "grey",
color_segment = list(basket_1 = "red"),
width_segment = list(basket_1 = 1),
linetype_segment = list(basket_1 = "solid"))
fori_plot
## End(Not run)