Introduction | Key Capabilities | New Workflow Overview | Setup | New SGWT Workflow Demonstration | Generate Example Pattern | Visualize Input Pattern | Step 1: Initialize SGWT Object | Step 2: Build Spectral Graph | Visualize Fourier Modes (Eigenvectors) | Step 3: Run SGWT Analysis | Visualize SGWT Decomposition | Energy Analysis | Advanced Features Demonstration | Different Wavelet Kernels | Step 4: Pattern Similarity Analysis | Low-frequency Only Analysis | Multiple Signal Analysis | Similarity Space Visualization with Multiple Patterns | Advanced Workflow Features | Custom Parameters | Summary | Key Takeaways | New Workflow Benefits | Parameter Guidelines | Next Steps
Package: BioGSP 1.0.0
Yuzhou Chang
BioGSP: Biological Graph Signal Processing for Spatial Data Analysis
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) <doi:10.1016/j.acha.2010.04.005>. 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) <doi:10.1101/2024.12.20.629650>.
Authors:
BioGSP_1.0.0.tar.gz
BioGSP_1.0.0.zip(r-4.7)BioGSP_1.0.0.zip(r-4.6)BioGSP_1.0.0.zip(r-4.5)
BioGSP_1.0.0.tgz(r-4.6-any)BioGSP_1.0.0.tgz(r-4.5-any)
BioGSP_1.0.0.tar.gz(r-4.7-any)BioGSP_1.0.0.tar.gz(r-4.6-any)
BioGSP_1.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
BioGSP/json (API)
| # Install 'BioGSP' in R: |
| install.packages('BioGSP', repos = c('https://bmengineer.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/bmengineer/biogsp/issues
Datasets:
- codex_toy_data - Toy CODEX Spatial Cell Type Data
Last updated from:5ed12ed48d. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 154 | ||
| source / vignettes | OK | 197 | ||
| linux-release-x86_64 | OK | 137 | ||
| macos-release-arm64 | OK | 205 | ||
| macos-oldrel-arm64 | OK | 155 | ||
| windows-devel | OK | 92 | ||
| windows-release | OK | 98 | ||
| windows-oldrel | OK | 89 | ||
| wasm-release | OK | 150 |
Exports:cal_laplaciancheckKbandcompare_kernel_familiescompute_sgwt_filterscosine_similaritydemo_sgwtFastDecompositionLapfind_knee_pointgfthello_sgwtigftinitSGWTplot_FMplot_sgwt_decompositionrunSGCCrunSGWTrunSpecGraphsgwt_auto_scalessgwt_energy_analysissgwt_forwardsgwt_get_kernelssgwt_inversesimulate_checkerboardsimulate_moving_circlessimulate_multiscalesimulate_multiscale_overlapsimulate_stripe_patternsvisualize_checkerboardvisualize_moving_circlesvisualize_multiscalevisualize_sgwt_kernelsvisualize_similarity_xyvisualize_stripe_patterns
Dependencies:clicpp11dplyrfarvergenericsggplot2gluegridExtragtableigraphisobandlabelinglatticelifecyclemagrittrMatrixpatchworkpillarpkgconfigR6RANNRColorBrewerRcppRcppEigenrlangRSpectraS7scalestibbletidyselectutf8vctrsviridisviridisLitewithr
