Learn R Programming

BioGSP (version 1.0.0)

Biological Graph Signal Processing for Spatial Data Analysis

Description

Implementation of Graph Signal Processing (GSP) methods including Spectral Graph Wavelet Transform (SGWT) for analyzing spatial patterns in biological data. Based on Hammond, Vandergheynst, and Gribonval (2011) . Provides tools for multi-scale analysis of biology spatial signals, including forward and inverse transforms, energy analysis, and visualization functions tailored for biological applications. Biological application example is on Stephanie, Yao, Yuzhou (2024) .

Copy Link

Version

Install

install.packages('BioGSP')

Version

1.0.0

License

GPL-3

Issues

0

Pull Requests

0

Stars

4

Forks

1

Maintainer

Yuzhou Chang

Last Published

February 2nd, 2026

Functions in BioGSP (1.0.0)

plot_FM

Plot Fourier modes (eigenvectors) from SGWT object
sgwt_get_kernels

Get a unified kernel family (low-pass and band-pass) by kernel_type
visualize_stripe_patterns

Visualize Stripe Pattern Simulation Results
sgwt-globals

Global variables used in ggplot2 aesthetics
visualize_multiscale

Visualize Multi-center Multi-scale Concentric Ring Patterns
sgwt_auto_scales

Generate automatic scales for SGWT
visualize_moving_circles

Visualize Moving Circles Pattern
visualize_checkerboard

Visualize checkerboard pattern
sgwt_inverse

Inverse SGWT transform (single or batch)
simulate_checkerboard

Simulate checkerboard pattern
simulate_stripe_patterns

Simulate Stripe Patterns
simulate_moving_circles

Simulate Moving Circles Pattern
visualize_similarity_xy

Visualize similarity in low vs non-low frequency space
print.SGWT

Print method for SGWT objects
runSGCC

Run SGCC weighted similarity analysis in Fourier domain
simulate_multiscale

Simulate Multi-center Multi-scale Concentric Ring Patterns
simulate_multiscale_overlap

Simulate Multiple Center Patterns with Fixed Centers
visualize_sgwt_kernels

Visualize SGWT kernels and scaling functions
plot_sgwt_decomposition

Plot SGWT decomposition results
cosine_similarity

Calculate cosine similarity between two vectors
BioGSP-package

BioGSP: Biological Graph Signal Processing for Spatial Data Analysis
checkKband

Check K-band limited property of signals
compare_kernel_families

Compare different kernel families
FastDecompositionLap

Fast eigendecomposition of Laplacian matrix
gft

Graph Fourier Transform
compute_sgwt_filters

Compute SGWT filters
demo_sgwt

Demo function for SGWT
igft

Inverse Graph Fourier Transform
cal_laplacian

Calculate Graph Laplacian Matrix
find_knee_point

Find knee point in a curve
initSGWT

Initialize SGWT object
hello_sgwt

Hello function for SGWT package demonstration
sgwt_energy_analysis

Analyze SGWT energy distribution across scales in Fourier domain
runSGWT

Run SGWT forward and inverse transforms for all signals
codex_toy_data

Toy CODEX Spatial Cell Type Data
sgwt_forward

Forward SGWT transform (single or batch)
runSpecGraph

Build spectral graph for SGWT object