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Plot an augmented p-rep design grid

Source: R/augmented_prep.R
plot_augmented_prep_design.Rd

Draws one field map per location for an augmented p-rep design.

Usage

plot_augmented_prep_design(
  design,
  locations = NULL,
  label = c("all_entries", "entry_type", "repeated_at", "block", "replicate", "none"),
  fill = c("entry_type", "is_extra_repeat", "repeated_at", "block", "replicate"),
  show_plot_labels = TRUE,
  show_block_labels = FALSE,
  block_label_position = c("background", "center"),
  label_cex = NULL,
  block_label_cex = NULL,
  block_label_col = NULL,
  block_lwd = 2,
  main = NULL,
  legend = TRUE,
  caption = TRUE,
  ...
)

Arguments

design

An object returned by augmented_prep_design() or its design data frame.

locations

Optional character vector of locations to plot. Defaults to all locations in design order.

label

Cell label to show. Use "all_entries", "entry_type", "repeated_at", "block", "replicate", or "none".

fill

Cell coloring variable. Use "entry_type", "is_extra_repeat", "repeated_at", "block", or "replicate".

show_plot_labels

Logical. If TRUE, labels are printed inside cells unless label = "none".

show_block_labels

Logical. If TRUE, block numbers are printed. Defaults to FALSE so block labels do not overlap accession labels.

block_label_position

Position for block labels when show_block_labels = TRUE. Use "background" for a faint watermark behind accession labels or "center" for a regular center label.

label_cex

Optional text size for plot-cell labels.

block_label_cex

Optional text size for block labels.

block_label_col

Color for block labels.

block_lwd

Line width for block boundaries.

main

Optional plot title. If multiple locations are plotted, a single value is combined with the location name; a vector matching the number of locations is used panel by panel.

legend

Logical. If TRUE, draw a legend for cell colors.

caption

Logical. If TRUE, print a short explanation of the colours and lines under each map.

...

Additional arguments passed to graphics::plot.window().

Value

Invisibly returns the plotted design data frame with internal plotting coordinates.

Details

A p-rep design has no check plots: at each location some entries are planted more than once (repeated entries), and these replace the checks for estimating the error and the block effects. By default the map colours the repeated entries (orange, names in bold) and the entries with a single plot at that location (light grey). Thick black lines outline the incomplete blocks; in resolvable designs a thick blue line separates the replicates, which are labelled at the right. A caption under each map explains this.

Examples

design <- augmented_prep_design(
  treatments = paste0("G", seq_len(12)),
  locations = c("Loc1", "Loc2", "Loc3"),
  block_size = 5,
  n_candidates = 5,
  seed = 123,
  field_cols = 5
)

plot_augmented_prep_design(design)