Package installation | Data loading | Specifying the cell subset of interest | Selection from low-dimensional plot | Clustering | Running Hypergate | Interpreting and polishing the results | Gating datapoints | Examining the output | Channels contributions | Reoptimize strategy | Human-readable output | Final notes | Which channels to use as input? | How big can the input matrix be?
Package: hypergate 0.8.5
Etienne Becht
hypergate: Machine Learning of Hyperrectangular Gating Strategies for High-Dimensional Cytometry
Given a high-dimensional dataset that typically represents a cytometry dataset, and a subset of the datapoints, this algorithm outputs an hyperrectangle so that datapoints within the hyperrectangle best correspond to the specified subset. In essence, this allows the conversion of clustering algorithms' outputs to gating strategies outputs.
Authors:
hypergate_0.8.5.tar.gz
hypergate_0.8.5.tar.gz(r-4.7-any)hypergate_0.8.5.tar.gz(r-4.6-any)
hypergate_0.8.5.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
hypergate/json (API)
| # Install 'hypergate' in R: |
| install.packages('hypergate', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- Samusik_01_subset - 2000 events randomly sampled from the 'Samusik_01' dataset
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated from:8eb34092ba. Checks:4 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 136 | ||
| source / vignettes | OK | 180 | ||
| linux-release-x86_64 | OK | 141 | ||
| wasm-release | OK | 177 |
Exports:boolmatchannels_contributionscolor_biplot_by_discreteF_betagate_from_biplothgate_infohgate_phenohgate_rulehgate_samplehypergateplot_gating_strategyreoptimize_strategysubset_matrix_hg
Dependencies:
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| boolmat | boolmat |
| channels_contributions | channels_contributions |
| Colors a biplot according to a vector with discrete values | color_biplot_by_discrete |
| contract | contract |
| contract.update | contract.update |
| coreloop | coreloop |
| Wrapper to locator that plots segments on the fly | en.locator |
| expand | expand |
| expand.update | expand.update |
| f | f |
| F_beta | F_beta |
| fill_FNTN_matrix | fill_FNTN_matrix |
| FNTN_matrix.recycle | FNTN_matrix.recycle |
| gate_from_biplot | gate_from_biplot |
| hgate_info | hgate_info |
| hgate_pheno | hgate_pheno |
| hgate_rule | hgate_rule |
| hgate_sample | hgate_sample |
| hypergate | hypergate |
| plot_gating_strategy | plot_gating_strategy |
| Remove self intersection in polygons | polygon.clean |
| reoptimize_strategy | reoptimize_strategy |
| 2000 events randomly sampled from the 'Samusik_01' dataset | Samusik_01_subset |
| subset_matrix_hg | subset_matrix_hg |
| Updates a gate vector | update_gate |