biosurvey (version 0.1.1)

plot_blocks_EG: Representation of environmental blocks in geography and environment

Description

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)
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)

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".

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

# NOT RUN {
# Data
data("m_matrix", 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)
# }