What is a clustering tree? | A simple example | The data | Plotting a tree | Controlling aesthetics | SC3 stability index | Layout | Adding labels | Clustering trees for scRNA-seq data | SingleCellExperiment objects | Seurat objects | Using genes as aesthetics | Overlaying clustering trees | Choosing what to colour | Labelling nodes | Showing the side view | Modifying appearance | Legends | Citing clustree | References
Package: clustree 0.5.1
clustree: Visualise Clusterings at Different Resolutions
Deciding what resolution to use can be a difficult question when approaching a clustering analysis. One way to approach this problem is to look at how samples move as the number of clusters increases. This package allows you to produce clustering trees, a visualisation for interrogating clusterings as resolution increases.
Authors:
clustree_0.5.1.tar.gz
clustree_0.5.1.zip(r-4.7)clustree_0.5.1.zip(r-4.6)clustree_0.5.1.zip(r-4.5)
clustree_0.5.1.tgz(r-4.6-any)clustree_0.5.1.tgz(r-4.5-any)
clustree_0.5.1.tar.gz(r-4.7-any)clustree_0.5.1.tar.gz(r-4.6-any)
clustree_0.5.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
clustree/json (API)
| # Install 'clustree' in R: |
| install.packages('clustree', repos = c('https://lazappi.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/lazappi/clustree/issues
Pkgdown/docs site:https://lazappi.github.io
Datasets:
- nba_clusts - Clustered NBA positions dataset
- sc_example - Simulated scRNA-seq dataset
clusteringclustering-treesvisualisationvisualization
Last updated from:24900bdf45. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 236 | ||
| source / vignettes | OK | 300 | ||
| linux-release-x86_64 | OK | 200 | ||
| macos-release-arm64 | OK | 129 | ||
| macos-oldrel-arm64 | OK | 130 | ||
| windows-devel | OK | 274 | ||
| windows-release | OK | 149 | ||
| windows-oldrel | OK | 145 | ||
| wasm-release | OK | 167 |
Exports:clustreeclustree_overlay
Dependencies:backportsbase64enccachemcheckmateclicpp11dplyrfarverfastmapgenericsggforceggplot2ggraphggrepelgluegraphlayoutsgridExtragtableigraphisobandjsonlitelabelinglatticelifecyclemagrittrMASSMatrixmemoisepillarpkgconfigpolyclippurrrR6RColorBrewerRcppRcppArmadillorlangS7scalesstringistringrsystemfontstibbletidygraphtidyrtidyselecttweenrutf8vctrsviridisviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Clustree | clustree-package |
| Plot a clustering tree | clustree clustree.data.frame clustree.matrix clustree.Seurat clustree.seurat clustree.SingleCellExperiment |
| Overlay a clustering tree | clustree_overlay clustree_overlay.data.frame clustree_overlay.matrix clustree_overlay.Seurat clustree_overlay.seurat clustree_overlay.SingleCellExperiment |
| Clustered NBA positions dataset | nba_clusts |
| Simulated scRNA-seq dataset | sc_example |
