% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/visped.R
\name{visped}
\alias{visped}
\title{Visualize a tidy pedigree}
\usage{
visped(
  ped,
  compact = FALSE,
  outline = FALSE,
  cex = NULL,
  showgraph = TRUE,
  file = NULL,
  highlight = NULL,
  trace = FALSE,
  showf = FALSE,
  labelvar = NULL,
  shapeby = c("sex", "role"),
  pagewidth = 200,
  symbolsize = 1,
  maxiter = 1000,
  genlab = FALSE,
  genlabcex = NULL,
  ...
)
}
\arguments{
\item{ped}{A \code{tidyped} object (which inherits from \code{data.table}). It is recommended that the pedigree is tidied and pruned by candidates using the \code{\link{tidyped}} function with the non-null parameter \code{cand}.}

\item{compact}{A logical value indicating whether terminal, non-parent
full-sib individuals will be replaced by one family display node. For
example, 100 eligible full siblings are shown as \code{"FS×100"} when
\code{compact = TRUE}. Highlighted individuals are not compacted, and the
underlying pedigree is unchanged. The default value is FALSE.}

\item{outline}{A logical value indicating whether shapes without labels will be shown. A graph of the pedigree without individual labels is shown when setting \code{outline = TRUE}. This is useful for viewing the pedigree outline and identifying immigrant individuals in each generation when the graph width exceeds the maximum PDF width (500 inches). The default value is FALSE.}

\item{cex}{NULL or a numeric value changing the size of individual labels shown in the graph. \emph{cex} is an abbreviation for 'character expansion factor'. The \code{visped} function will attempt to estimate (\code{cex=NULL}) the appropriate cex value and report it in the messages. Based on the reported cex from a previous run, this parameter should be increased if labels are wider than their shapes in the PDF; conversely, it should be decreased if labels are narrower than their shapes. The default value is NULL.}

\item{showgraph}{A logical value indicating whether a plot will be shown in the default graphic device (e.g., the Plots panel in RStudio). This is useful for quick viewing without opening a PDF file. However, the graph on the default device may not be legible (e.g., overlapping labels or aliasing lines) due to size restrictions. It is recommended to set \code{showgraph = FALSE} for large pedigrees. The default value is TRUE.}

\item{file}{NULL or a character value specifying whether the pedigree graph will be saved as a vector file. Files ending in '.svg' are written with the SVG device; all other file names use PDF output. The vector output is legible and avoids overlapping labels even with many individuals or long labels. It is recommended to save the pedigree graph as a vector file. The default value is NULL.}

\item{highlight}{NULL, a character vector of individual IDs, or a list specifying individuals to highlight. If a character vector is provided, individuals will be highlighted with a purple border while preserving their sex-based fill color. If a list is provided, it should contain:
\itemize{
  \item \code{ids}: (required) character vector of individual IDs to highlight.
  \item \code{frame.color}: (optional) hex color for the border of focal individuals.
  \item \code{color}: (optional) hex color for the fill of focal individuals.
  \item \code{rel.frame.color}: (optional) hex color for the border of relatives (used when \code{trace} is not NULL).
  \item \code{rel.color}: (optional) hex color for the fill of relatives (used when \code{trace} is not NULL).
}
For example: \code{c("A", "B")} or \code{list(ids = c("A", "B"), frame.color = "#9c27b0")}. The function will check if the specified individuals exist in the pedigree and issue a warning for any missing IDs. The default value is NULL.}

\item{trace}{A logical value or a character string. If TRUE, all ancestors and descendants of the individuals specified in \code{highlight} will be highlighted. If a character string, it specifies the tracing direction: "\strong{up}" (ancestors), "\strong{down}" (descendants), or "\strong{all}" (union of ancestors and descendants). This is useful for focusing on specific families within a large pedigree. The default value is FALSE.}

\item{showf}{A logical value indicating whether inbreeding coefficients will be shown in the graph. If \code{showf = TRUE} and the column \strong{f} is missing, \code{visped()} will try to compute it automatically with \code{\link{inbreed}} on a structurally complete pedigree. If automatic computation is not possible, a warning is issued and labels are drawn without \strong{f}. The default value is FALSE.}

\item{labelvar}{NULL, a single non-empty character value naming a column in
\code{ped}, or a character vector with one displayed label per input
pedigree row. Row-aligned vectors are attached before any internal
tidying or reordering. Compact full-sib family nodes still show family
size when \code{compact = TRUE}. Missing or empty values fall back to
individual IDs. The default value is NULL.}

\item{shapeby}{Character string controlling what node shapes encode.
\code{"sex"} (default) uses circles for females, squares for males,
diamonds for unknown sex, and hexagons for monoecious individuals.
\code{"role"} distinguishes individual records from compact family
summaries by shape while keeping sex-based fill colors for real
individuals. Compact family summaries are rectangles in both modes.}

\item{pagewidth}{A numeric value specifying the width of the PDF file in inches. This controls the horizontal scaling of the layout. The default value is 200.}

\item{symbolsize}{A numeric value specifying the scaling factor for node size relative to the label size. Values greater than 1 increase the node size (adding padding around the label), while values less than 1 decrease it. This is useful for fine-tuning the whitespace and legibility of dense graphs. The default value is 1.}

\item{maxiter}{An integer specifying the maximum number of iterations for the Sugiyama layout algorithm to minimize edge crossings. Higher values (e.g., 2000 or 5000) may result in fewer crossed lines for complex pedigrees but will increase computation time. The default value is 1000.}

\item{genlab}{FALSE to omit generation labels; TRUE to draw the default
labels G1, G2, ...; or an unnamed, non-empty character vector of custom
labels. Custom labels are assigned from top to bottom to the final
displayed generation layers and must contain exactly one label per layer.
The default value is FALSE.}

\item{genlabcex}{NULL or a numeric value controlling the size of displayed
generation labels. If \code{NULL}, \code{visped()} uses an automatic size
based on node scaling. Set a larger value to keep generation labels
readable in deep pedigrees. The default value is NULL.}

\item{...}{Additional arguments passed to \code{\link[igraph:plot.igraph]{plot.igraph}}.}
}
\value{
The function mainly produces a plot on the current graphics device and/or a vector file. It invisibly returns a list containing the graph object, layout coordinates, and node sizes.
}
\description{
\code{visped} function draws a graph of a full or compact pedigree.
}
\details{
This function takes a pedigree tidied by the \code{\link{tidyped}} function and outputs a hierarchical graph for all individuals in the pedigree. The graph can be shown on the default graphic device or saved as a PDF or SVG file. The vector output is legible and avoids overlapping labels. It is especially useful when the number of individuals is large and individual labels are long.

Rendering is performed using a Two-Pass strategy: edges are drawn first to ensure center-to-center connectivity, followed by nodes and labels. This ensures perfect visual alignment in high-resolution vector outputs. The function also supports real-time ancestry and descendant highlighting.

This function can draw the graph of a very large pedigree (> 10,000 individuals per generation) by compacting full-sib individuals. It is highly effective for aquatic animal pedigrees, which usually include many full-sib families per generation in nucleus breeding populations. The outline of a pedigree without individual labels is still shown if the width of a pedigree graph exceeds the maximum width (500 inches) of the PDF file.

By default, \code{shapeby = "sex"} encodes individual sex with node shape:
females are circles, males are squares, individuals of unknown sex are
diamonds, and monoecious individuals are hexagons. Set
\code{shapeby = "role"} to use the legacy role-based scheme, where circles
represent individual records and green-grey rectangles represent compact
full-sib family summaries. Compact family summaries remain green-grey
rectangles in both modes. In \code{shapeby = "role"} mode, real individuals
remain circles, but their fill colors still encode sex. Dark sky blue
indicates males, dark goldenrod indicates females, teal indicates monoecious
individuals, and neutral grey indicates unknown sex. Purple borders indicate
highlighted individuals rather than sex.
}
\note{
Isolated individuals (those with no parents and no progeny, assigned Gen 0) are automatically filtered out and not shown in the plot. A message will be issued if any such individuals are removed.
}
\examples{
library(visPedigree)
library(data.table)
# Drawing a simple pedigree
simple_ped_tidy <- tidyped(simple_ped)
visped(simple_ped_tidy, 
       cex=0.25, 
       symbolsize=5.5)

# Use application-specific labels for the displayed generations.
# Custom labels are assigned from top to bottom.
generation_labels <- paste("Generation", sort(unique(simple_ped_tidy$Gen)))
visped(simple_ped_tidy,
       genlab = generation_labels,
       cex = 0.25,
       symbolsize = 5.5)

# Highlighting an individual and its ancestors and descendants
visped(simple_ped_tidy, 
       highlight = "J5X804", 
       trace = "all", 
       cex=0.25, 
       symbolsize=5.5)

# Showing inbreeding coefficients in the graph
simple_ped_tidy_inbreed <- tidyped(simple_ped, inbreed = TRUE)
visped(simple_ped_tidy_inbreed,
       showf = TRUE, 
       cex=0.25, 
       symbolsize=5.5)

# visped() will automatically compute inbreeding coefficients if 'f' is missing
visped(simple_ped_tidy,
       showf = TRUE,
       cex=0.25,
       symbolsize=5.5)

# Use the role-based legacy symbol scheme
visped(simple_ped_tidy,
       shapeby = "role",
       cex=0.25,
       symbolsize=5.5)

# Adjusting page width and symbol size for better layout
# Increase pagewidth to spread nodes horizontally in the pdf file
# Increase symbolsize for more padding around individual labels
visped(simple_ped_tidy, 
       cex=0.25, 
       symbolsize=5.5, 
       pagewidth = 100, 
       file = tempfile(fileext = ".pdf"))

# Saving pedigree as SVG with larger labels and tighter symbols
visped(simple_ped_tidy,
       cex=0.8,
       symbolsize=1,
       pagewidth = 100,
       file = tempfile(fileext = ".svg"))

# Highlighting multiple individuals with custom colors
visped(simple_ped_tidy,
       highlight = list(ids = c("J3Y620", "J1X971"),
                        frame.color = "#4caf50",
                        color = "#81c784"),
       cex=0.25,
       symbolsize=5.5)

# Handling large pedigrees: Saving to PDF is recommended for legibility
# The 'trace' and 'tracegen' parameters in tidyped() help prune the graph
cand_labels <- big_family_size_ped[(Year == 2007) & (substr(Ind,1,2) == "G8"), Ind]
\donttest{
big_ped_tidy <- tidyped(big_family_size_ped, 
                        cand = cand_labels, 
                        trace = "up", 
                        tracegen = 2)
# Use compact = TRUE for large families
visped(big_ped_tidy, 
       compact = TRUE, 
       cex=0.08, 
       symbolsize=5.5, 
       file = tempfile(fileext = ".pdf"))

# Use outline = TRUE if individual labels are not required
visped(big_ped_tidy, 
       compact = TRUE, 
       outline = TRUE, 
       file = tempfile(fileext = ".pdf"))
}

}
\seealso{
\code{\link{tidyped}} for tidying pedigree data (required input)
\code{\link{vismat}} for visualizing relationship matrices as heatmaps
\code{\link{pedmat}} for computing relationship matrices
\code{\link{splitped}} for splitting pedigree into connected components
\code{\link[igraph:plot.igraph]{plot.igraph}} underlying plotting function
}
