Representation of environmental blocks in geography and environment

Creates a plot representing environmental blocks (all or selected) in both spaces, environmental and/or geographic.

Usage

plot_blocks_EG(master, region_border = TRUE, mask_border = FALSE,
               which = "all", block_ID = FALSE, col_all = NULL,
               col_selected = NULL, col_ID = NULL, cex_all = 0.7,
               cex_selected = 1, cex_ID = 1, pch_all = 16,
               pch_selected = 16, add_main = TRUE, mar = NULL)

plot_blocks_E(master, which = "all", block_ID = FALSE, col_all = NULL,
              col_selected = NULL, col_ID = NULL, cex_all = 0.7,
              cex_selected = 1, cex_ID = 1, pch_all = 16,
              pch_selected = 16, main = "", xlab = NULL, ylab = NULL)

plot_blocks_G(master, region_border = TRUE, mask_border = FALSE,
              which = "all", block_ID = FALSE, col_all = NULL,
              col_selected = NULL, col_ID = NULL, cex_all = 0.7,
              cex_selected = 1, cex_ID = 1, pch_all = 16,
              pch_selected = 16, mar = NULL)

Arguments

master: master_matrix object derived from function prepare_master_matrix or master_selection object derived from functions uniformG_selection, uniformE_selection or EG_selection. Blocks must be defined, see make_blocks.
region_border: (logical) whether to add region border to the plot. Default = TRUE.
mask_border: (logical) whether to add mask border to the plot. Ignored if mask is not present in master_selection. Default = FALSE.
which: (character) blocks to be plotted. Options are "all" or "selected". Default = "all".
block_ID: (logical) whether to add a text ID to blocks plotted in environmental space. Default = FALSE.
col_all: colors for points in all blocks. The default, NULL, uses a color blind friendly palette to differentiate among distinct blocks when which = "all", or uses a light gray color when which = "selected". See details for explanations of how to define them.
col_selected: color for points in selected blocks. Ignored if which = "all". The default, NULL, uses a blue color to represent selected blocks on top of all.
col_ID: color for text ID to be added if block_ID = TRUE. The default, NULL, uses the "back".
cex_all: (numeric) value defining magnification of points in all blocks relative to the default. Default = 0.7.
cex_selected: (numeric) value defining magnification of points in selected blocks relative to the default. Default = 1.
cex_ID: (numeric) value defining magnification of text ID to be added if block_ID = TRUE. Default = 1.
pch_all: (numeric) integer specifying a symbol when plotting points of all blocks. Default = 16.
pch_selected: (numeric) integer specifying a symbol when plotting points of selected blocks. Default = 16.
add_main: (logical) whether or not to add fixed titles to the plot. Default = TRUE. Titles added are "Environmental space" and "Geographic space".
mar: (numeric) vector of length 4 to set the margins of the plot in G. The default, NULL, is (3.1, 3.1, 2.1, 2.1) for plot_blocks_G and (3.5, 0.5, 0.5, 0.5) for plot_blocks_EG.
main: (character) the main title for the plot.
xlab: (character) label for the x axis. The default, NULL, uses variable_1.
ylab: (character) label for the y axis. The default, NULL, uses variable_2.

Value

A plot showing all the blocks of the region of interest and, if asked, the blocks that were selected. They are show in both spaces, geographic and/or environmental.

Details

Defining colors in col_all depends on what is chosen in which. If "all" is chosen, it is convenient to define col_all as a color ramp palette (randomly arranged) or a set of colors depending on the number of blocks in the object defined in master. If "selected" is chosen in which it is recommended to use a single color, preferably a light one, so the selected blocks can be easily identified. See examples.

Examples

# Data
m_matrix <- read_master(system.file("extdata/m_matrix.rds",
                                    package = "biosurvey"))

# Creating blocks
m_blocks <- make_blocks(m_matrix, variable_1 = "PC1",
                        variable_2 = "PC2", n_cols = 10, n_rows = 10,
                        block_type = "equal_area")

plot_blocks_EG(master = m_blocks, block_ID = TRUE)

plot_blocks_E(master = m_blocks)

plot_blocks_G(master = m_blocks)


# Defining your own colors
n_blocks <- length(m_blocks$data_matrix$Block)
your_palette <- sample(heat.colors(n_blocks), n_blocks)
block_factor <- as.factor(m_blocks$data_matrix$Block)
your_colors <- your_palette[block_factor]

plot_blocks_EG(master = m_blocks, block_ID = TRUE, col_all = your_colors)