My_Imagine: Plot presence absence matirx with up to five associated...

In RodolfoPelinson/AtlanticForestMetacommunity: Gives the functions and data for the Analysis of Pelinson et al. 2021 "Disentangling the multiple drivers of amphibian metacommunity structure in the Atlantic Forest at multiple spatial scales"

Plot presence absence matirx with up to five associated environmental gradients.

Description

This function plots the incidence matrix, ordinated or not, with up to five associated environmental gradients associates.

Usage

My_Imagine(
  comm,
  col = c(0, 1, 2),
  order = TRUE,
  scores = 1,
  fill = TRUE,
  xlab = "",
  ylab = "",
  yline = 0,
  xline = 0,
  sitenames = rownames(comm),
  cex.envlab = 1,
  speciesnames = colnames(comm),
  xlab_line = 3,
  cex.xlab = 2,
  ylab_line = 3,
  cex.ylab = 2,
  main = "",
  main_line = 3,
  cex.main = 2,
  Env1 = NULL,
  Env2 = NULL,
  Env.col_1 = NULL,
  Env.label_1 = NULL,
  Env.col_2 = NULL,
  Env.label_2 = NULL,
  cex.site = 1,
  cex.species = 1,
  top_margin = 2,
  left_margin = 2,
  bottom_margin = 3,
  right_margin = 1,
  EigenVal = F,
  box.lwd = 1,
  Env.col_3 = NULL,
  Env.label_3 = NULL,
  Env3 = NULL,
  Env.col_4 = NULL,
  Env.label_4 = NULL,
  Env4 = NULL,
  Env.col_5 = NULL,
  Env.label_5 = NULL,
  Env5 = NULL
)

Arguments

comm	An incidence matrix.
col	The colors of absences, true presences and filled presences, respectively.
order	Logical. Should the matrix be order by reciprocal averaging (CA)? Defaut set is to TRUE.
scores	Numeric. What axis of the CA should be used for ordination? Defaut is 1.
fill	Logical. Should embeded absences be filled?
xlab	Label of the x axis
ylab	Label of the y axis
yline	Line position of y label. Defaut is 2.
xline	Line position of x label. Defaut is 2.
sitenames	A vector of site Names. Defaut is row names.
cex.envlab	The size of the environmental gradient labels
speciesnames	A vector of species Names. Defaut is column names.
xlab_line	Line position of the x label
cex.xlab	Size of the x label
ylab_line	Line position of the y label
cex.ylab	Size of the y label
main	Main Title
main_line	Line poisition of the main title.
cex.main	Size of the main title
Env1	The first environmental gradient
Env2	The second environmental gradient.
Env.col_1	The colors of the first Environmental Gradient. If it is a continuous gradient, this should be a vector with the two most extreme colors. If it is a factor, it should be a vector with one color for each of the levels of the factor.
Env.label_1	Name of the first environmental gradient.
Env.col_2	The colors of the second Environmental Gradient. If it is a continuous gradient, this should be a vector with the two most extreme colors. If it is a factor, it should be a vector with one color for each of the levels of the factor.
Env.label_2	Name of the second environmental gradient.
cex.site	The size of the site labels.
cex.species	The size of the species labels.
top_margin	The space left in the top of the plot. Useful to fit long species names.
left_margin	The space left in the left side of the plot. Useful to fit long site names.
bottom_margin	The space left in the bottom side of the plot.
right_margin	The space left in the right side of the plot.
EigenVal	Should the relative eigenvalue of the ordination axis used be plotted?
box.lwd	The width of the plot box.
Env.col_3	The colors of the third Environmental Gradient. If it is a continuous gradient, this should be a vector with the two most extreme colors. If it is a factor, it should be a vector with one color for each of the levels of the factor.
Env.label_3	Name of the third environmental gradient.
Env3	The third environmental gradient.
Env.col_4	The colors of the fourth Environmental Gradient. If it is a continuous gradient, this should be a vector with the two most extreme colors. If it is a factor, it should be a vector with one color for each of the levels of the factor.
Env.label_4	Name of the fourth environmental gradient.
Env4	The fourth environmental gradient.
Env.col_5	The colors of the fifth Environmental Gradient. If it is a continuous gradient, this should be a vector with the two most extreme colors. If it is a factor, it should be a vector with one color for each of the levels of the factor.
Env.label_5	Name of the fifth environmental gradient.
Env5	The fifth environmental gradient.

RodolfoPelinson/AtlanticForestMetacommunity documentation built on Aug. 5, 2023, 3:53 p.m.