In bioinfoDZ/Stereo3D: Stereo3D: Using stereo images to enrich 3D visualization

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1. Introduction:

Visualization in three-dimensional (3D) space is a standard and critical process for examining the complex structure of high dimensional data. Stereo imaging technology can be adopted to enhance 3D representation of any complex data, especially those consisting mostly of points and lines. We illustrate the simple steps that are involved and strongly encourage others to implement it in their own visualization software. To facilitate its application, we have also created a new software that can convert a regular 3D scatterplot or network figure to a stereo image

2. Concept:

When 2D-image of original data and the slightly rotated data are viewed side by side a 3D illusion is created due to two perspectives of the same object.

The original set of coordinates $(X, Y, Z)$ can be rotated (counter-clockwise direction) by an angle $\theta$ along Y-axis using the rotation matrix $R_y (\theta)$. The new set of coordinates is obtained as

$$ \begin{aligned} \begin{bmatrix} X^\\ Y^ \ Z^` \ 1 \end{bmatrix} & = R_y (\theta) \cdot \begin{bmatrix} X \ Y \ Z \ 1 \end{bmatrix} \ & = \begin{pmatrix} cos \theta & 0 & -sin \theta & 0\ 0 & 1 & 0 & 0\ sin \theta & 0 & cos \theta & 0\ 0 & 0 & 0 & 1 \end{pmatrix} \cdot \begin{bmatrix} X \ Y \ Z \ 1 \end{bmatrix} \end{aligned} $$

3. Availability and Installation

The development version of Stereo3D package is available at https://github.com/bioinfoDZ/Stereo3D and can be installed as

# install.packages("devtools")
devtools::install_github("bioinfoDZ/Stereo3D",build_vignettes = FALSE )

4. Functions

4.1 Stereo3D

Description

Create Stereoscopic 3D image of the given data.

Usage

Stereo3D(data_file=sample_data_file, stereo_angle, distance, connection_file)

Arguments

data_file: A tab seperated file with ".tsv" extension and having five columns (index, X, Y, Z and Color) of the data. Where, X, Y and Z represent cordinates of a datapoint, Color is the label of the given data point and index clolumn have the index information of the datapoints.
stereo_angle: angle by which 3D data to be rotated along Y-axis. Default: 5 degree
distance: Distance or gap between the two stereo images.
connection_file: A tab seperated file (optional). Where, first and second column has indices of start and end points (from data_file) of a connection respectively.

Details

The dataset is rotatated by a given angle along the Y-axis and a Stereoscopic 3D scatter plot image is created.

Value

Create Stereoscopic 3D plot with input data filename prefix and _Stereo.pdf extention.
Interactive 3D plot for the above image pops up, which can be zoomed and rotated by draging the mouse.

Examples

> connection_fileName=system.file("extdata", "connection_file.tsv",
package = "Stereo3D", mustWork = TRUE)
> sample_data_file=system.file("extdata", "sample_3D_data.tsv",
package = "Stereo3D", mustWork = TRUE)

> Stereo3D(data_file=sample_data_file, stereo_angle=5, distance=0,
connection_file=connection_fileName) # dataset stereo image is created
and saved as "sample_3D_data_Stereo.pdf", another interactive 3D image also pops-up.