plot_3d_mapping: Create 3D Visualization

In topolow: Force-Directed Euclidean Embedding of Dissimilarity Data

Create 3D Visualization

Description

Creates an interactive or static 3D visualization using rgl. Supports both temporal and cluster-based coloring schemes with configurable point appearances and viewing options.

Usage

plot_3d_mapping(
  df,
  ndim,
  dim_config = new_dim_reduction_config(),
  aesthetic_config = new_aesthetic_config(),
  layout_config = new_layout_config(),
  interactive = TRUE,
  output_dir
)

Arguments

df	Data frame containing: - V1, V2, ... Vn: Coordinate columns - antigen: Binary indicator for antigen points - antiserum: Binary indicator for antiserum points - cluster: (Optional) Factor or integer cluster assignments - year: (Optional) Numeric year values for temporal coloring
ndim	Number of dimensions in input coordinates (must be >= 3)
dim_config	Dimension reduction configuration object
aesthetic_config	Aesthetic configuration object
layout_config	Layout configuration object
interactive	Logical; whether to create an interactive plot
output_dir	Character. Directory for output files. Required if interactive is FALSE.

Details

The function supports two main visualization modes:

1. Interactive mode: Creates a manipulatable 3D plot window

2. Static mode: Generates a static image from a fixed viewpoint

Color schemes are automatically selected based on available data:

• If cluster data is present: Uses discrete colors per cluster

• If year data is present: Uses continuous color gradient

• Otherwise: Uses default point colors

For data with more than 3 dimensions, dimension reduction is applied first.

Note: This function requires the rgl package and OpenGL support. If rgl is not available, the function will return a 2D plot with a message explaining how to enable 3D visualization.

Value

Invisibly returns the rgl scene ID for further manipulation if rgl is available, or a 2D ggplot object as a fallback.

See Also

plot_temporal_mapping for 2D temporal visualization plot_cluster_mapping for 2D cluster visualization make_interactive for converting 2D plots to interactive versions

Examples

# Create sample data
set.seed(123)
data <- data.frame(
  V1 = rnorm(100), V2 = rnorm(100), V3 = rnorm(100), V4 = rnorm(100), name = 1:100,
  antigen = rep(c(0,1), 50), antiserum = rep(c(1,0), 50),
  cluster = rep(1:5, each=20), year = rep(2000:2009, each=10)
)

# Create a static plot and save to a temporary file
# This example requires an interactive session and the 'rgl' package.
if (interactive() && requireNamespace("rgl", quietly = TRUE)) {
  temp_dir <- tempdir()
  # Basic interactive plot (will open a new window)
  if(interactive()) {
    plot_3d_mapping(data, ndim=4)
  }

# Custom configuration for temporal visualization
aesthetic_config <- new_aesthetic_config(
  point_size = 5,
  point_alpha = 0.8,
  gradient_colors = list(
    low = "blue",
    high = "red"
  )
)

layout_config <- new_layout_config(
  width = 12,
  height = 12,
  background_color = "black",
  show_axis = TRUE
)
  # Create customized static plot and save it
plot_3d_mapping(data, ndim=4,
  aesthetic_config = aesthetic_config,
  layout_config = layout_config,
  interactive = FALSE, output_dir = temp_dir
)
  list.files(temp_dir)
  unlink(temp_dir, recursive = TRUE)
}

topolow documentation built on Aug. 31, 2025, 1:07 a.m.