Package: hilbertSimilarity 0.4.3.9000
hilbertSimilarity: Hilbert Similarity Index for High Dimensional Data
Quantifying similarity between high-dimensional single cell samples is challenging, and usually requires some simplifying hypothesis to be made. By transforming the high dimensional space into a high dimensional grid, the number of cells in each sub-space of the grid is characteristic of a given sample. Using a Hilbert curve each sample can be visualized as a simple density plot, and the distance between samples can be calculated from the distribution of cells using the Jensen-Shannon distance. Bins that correspond to significant differences between samples can identified using a simple bootstrap procedure.
Authors:
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hilbertSimilarity.pdf |hilbertSimilarity.html✨
hilbertSimilarity/json (API)
# Install 'hilbertSimilarity' in R: |
install.packages('hilbertSimilarity', repos = c('https://yannabraham.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/yannabraham/hilbertsimilarity/issues
Last updated 5 years agofrom:a54c0a7eb1. Checks:OK: 1 NOTE: 8. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Nov 03 2024 |
R-4.5-win-x86_64 | NOTE | Nov 03 2024 |
R-4.5-linux-x86_64 | NOTE | Nov 03 2024 |
R-4.4-win-x86_64 | NOTE | Nov 03 2024 |
R-4.4-mac-x86_64 | NOTE | Nov 03 2024 |
R-4.4-mac-aarch64 | NOTE | Nov 03 2024 |
R-4.3-win-x86_64 | NOTE | Nov 03 2024 |
R-4.3-mac-x86_64 | NOTE | Nov 03 2024 |
R-4.3-mac-aarch64 | NOTE | Nov 03 2024 |
Exports:add.cutandrewsProjectiondo.cutdo.hilberthilbert.orderhilbertProjectionjs.distlocalMaximalocalMinimamake.cutshow.cut
Comparing Samples using hilbertSimilarity
Rendered fromcomparing_samples.Rmd
usingknitr::rmarkdown
on Nov 03 2024.Last update: 2019-10-29
Started: 2016-02-23
Identifying Treatment effects using hilbertSimilarity
Rendered fromidentifying_effects.Rmd
usingknitr::rmarkdown
on Nov 03 2024.Last update: 2019-10-29
Started: 2016-02-23
Readme and manuals
Help Manual
Help page | Topics |
---|---|
Add New Cut Thresholds | add.cut |
Use Andrews plots to visualize the Hilbert curve | andrewsProjection |
Apply Cuts to the Reference Matrix | do.cut |
Generate the Hilbert Index from a Cut Reference Matrix | do.hilbert |
Estimate the Hilbert order for a given matrix | hilbert.order |
Map High Dimensional Coordinates to Hilbert Index and back | hilbertMapping |
Project a Cut Reference Matrix to a Different Space through an Hilbert Index | hilbertProjection |
Hilbert Similarity Index for High Dimensional Data | hilbertSimilarity-package hilbertSimilarity |
Compute the Jensen-Shannon Distance between 2 sets of Hilbert Index | js.dist |
Find Local Maxima in a vector | localMaxima |
Find Local Minima in a vector | localMinima |
Generate Cutting Points for a Multidimensional Matrix | make.cut |
Plot the cuts generated through make.cut | show.cut |