Description | Installation | Dependencies | Input File Preparation | Basic Workflow | 1. Load required packages and data | 2. Normalize spatial coordinates | 3. Merge spatial and metadata information | 4. Calculate nearest distances between cell types | 5. Compare distance among subgroups | 6. Create radial network visualization | 7. Spatial visualization of interactions | 8. Correlation analysis | Applications | Limitations | Troubleshooting | Citation | Contact | License
Package: STDistance 0.6.8
STDistance: Spatial Transcriptomics Distance Calculation and Visualization
Analysis of spatial relationships between cell types in spatial transcriptomics data. Spatial proximity is a critical factor in cell-cell communication. The package calculates nearest neighbor distances between specified cell types and provides visualization tools to explore spatial patterns. Applications include studying cell-cell interactions, immune microenvironment characterization, and spatial organization of tissues.
Authors:
STDistance_0.6.8.tar.gz
STDistance_0.6.8.zip(r-4.7)STDistance_0.6.8.zip(r-4.6)STDistance_0.6.8.zip(r-4.5)
STDistance_0.6.8.tgz(r-4.6-any)STDistance_0.6.8.tgz(r-4.5-any)
STDistance_0.6.8.tar.gz(r-4.7-any)STDistance_0.6.8.tar.gz(r-4.6-any)
STDistance_0.6.8.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
STDistance/json (API)
| # Install 'STDistance' in R: |
| install.packages('STDistance', repos = c('https://princewang2018.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- distance_results - Distance_results
- metadata - Metadata
- posi - Posi
- tissue_posi - Tissue_posi
- tissue_posi_normalized - Tissue_posi_normalized
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated from:013c1b89e7. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 166 | ||
| source / vignettes | OK | 185 | ||
| linux-release-x86_64 | OK | 166 | ||
| macos-release-arm64 | OK | 145 | ||
| macos-oldrel-arm64 | OK | 89 | ||
| windows-devel | OK | 110 | ||
| windows-release | OK | 100 | ||
| windows-oldrel | OK | 149 | ||
| wasm-release | OK | 143 |
Exports:calculate_correlationscalculate_nearest_distancesnormalize_spatialplot_distance_boxplotplot_radial_distancevisualize_spatial_gradientvisualize_spatial_multinetworkvisualize_spatial_network
Dependencies:backportsbase64encbslibcachemcheckmatecliclustercolorspacecpp11data.tabledigestdplyrevaluatefarverfastmapfontawesomeforeignFormulafsgenericsggplot2gluegridExtragtablehighrHmischtmlTablehtmltoolshtmlwidgetsisobandjquerylibjsonliteknitrlabelinglifecyclemagrittrmemoisemimennetpillarpkgconfigpurrrR6rappdirsRColorBrewerrlangrmarkdownrpartrstudioapiS7sassscalesstringistringrtibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunyaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Perform correlation analysis between spatial features and distance metrics with visualization | calculate_correlations |
| Calculate nearest distances between cell types | calculate_nearest_distances |
| distance_results | distance_results |
| Metadata | metadata |
| Normalize spatial coordinates | normalize_spatial |
| Visualize Nearest Neighbor Distances with Boxplot and Mean ± SEM | plot_distance_boxplot |
| Radial Distance Visualization with Collision Avoidance | plot_radial_distance |
| posi | posi |
| tissue_posi | tissue_posi |
| tissue_posi_normalized | tissue_posi_normalized |
| Visualize spatial network with expression gradient | visualize_spatial_gradient |
| Visualize spatial relationships between multiple cell types | visualize_spatial_multinetwork |
| Visualize spatial relationships between cell types | visualize_spatial_network |
