Introduction | The Mercator Class | UMAP | Euclideanization | Self-Organizing Maps | Warning | Conclusions | Appendix
Package: Mercator 1.1.7
Kevin R. Coombes
Mercator: Clustering and Visualizing Distance Matrices
Defines the classes used to explore, cluster and visualize distance matrices, especially those arising from binary data. See Abrams and colleagues, 2021, <doi:10.1093/bioinformatics/btab037>.
Authors:
Mercator_1.1.7.tar.gz
Mercator_1.1.7.tar.gz(r-4.7-any)Mercator_1.1.7.tar.gz(r-4.6-any)
Mercator_1.1.7.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
Mercator/json (API)
| # Install 'Mercator' in R: |
| install.packages('Mercator', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://r-forge.r-project.org/projects/oompa
Datasets:
- CML1000 - CML Cytogenetic Data
- CML500 - CML Cytogenetic Data
- fakeclin - CML Cytogenetic Data
- fakedata - CML Cytogenetic Data
- lgfFeatures - CML Cytogenetic Data
Last updated from:8b381841ed. Checks:4 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 236 | ||
| source / vignettes | OK | 251 | ||
| linux-release-x86_64 | OK | 251 | ||
| wasm-release | OK | 127 |
Exports:addVisualizationbarplotbinaryDistanceBinaryMatrixdownsamplegetClustershistMercatorplotreclusterrecolorremapColorsremoveDuplicateFeaturesremoveDuplicatesscattersetClustersshowtthreshLGF
Dependencies:ade4askpassBiobaseBiocGenericschangepointClassDiscoverycliclueclustercolorspacecpmcpp11dendextendfarverflexmixgenericsggplot2gluegridExtragtablehereigraphisobandjsonlitekernlabKernSmoothkohonenlabelinglatticelifecyclemagrittrMASSMatrixmclustmodeltoolsmovMFnnetoompaBaseoompaDataopensslPCDimensionpixmappkgconfigpngPolychromeR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenRcppTOMLreticulaterlangrprojrootRSpectraRtsneS7scalesscatterplot3dskmeansslamspsysThresherumapvctrsviridisviridisLitewithrzoo
UMAP and SOM from Distance Matrices
Last update: 2021-07-16
Started: 2021-07-16
Using the Mercator Package
Introduction | The BinaryMatrix Class | A Limited Sample Dataset | Generating the BinaryMatrix | Remove Duplicates | Data Filtering with Thresher | Visualization | Jaccard Distance | Hierarchical Clustering | t-Distributed Stochastic Neighbor Embedding | Multi-Dimensional Scaling | Silhouette-Width Barplots | iGraph | Cluster Identities | Sokal-Michener Metric | Changing the Color Palette | References
Last update: 2021-01-10
Started: 2019-08-02
Mercator for Continuous Data
Introduction | The Mercator Class | Visualization | Hierarchical Clustering | t-Distributed Stochastic Neighbor Embedding | Multi-Dimensional Scaling | iGraph | Cluster Identities | Silhouette-Width Barplots | Reclustering | Hierarchical Clusters | True Clusters | Appendix
Last update: 2020-08-24
Started: 2020-08-24
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Binary Distance Definitions Across Methods | binaryDistance goodmanKruskalDistance goodmanKruskalSimilarity hammingDistance jaccardDistance jaccardSimilarity pearsonDistance pearsonSimilarity russellRaoSimilarity russelRaoDistance sokalMichenerDistance sokalMichenerSimilarity |
| Class '"BinaryMatrix"' | BinaryMatrix BinaryMatrix-class dim,BinaryMatrix-method hist,BinaryMatrix-method print,BinaryMatrix-method show,BinaryMatrix-method summary,BinaryMatrix-method t,BinaryMatrix-method validBinaryMatrix [,BinaryMatrix,ANY,ANY,ANY-method |
| Downsampling a Distance Visualization to Facilitate iGraph | downsample |
| The 'Mercator' Distance Visualization Object | addVisualization barplot,Mercator-method dim,Mercator-method getClusters hist,Mercator-method Mercator Mercator-class plot,Mercator,missing-method scatter,Mercator-method summary,Mercator-method [,Mercator,ANY,ANY,ANY-method |
| CML Cytogenetic Data | CML1000 CML500 fakeclin fakedata lgfFeatures mercator-data |
| Remove Duplicate Features or Samples from a Binary Matrix Object | removeDuplicateFeatures removeDuplicates |
| Changing Cluster and Color Assignments in Mercator | recluster recolor remapColors setClusters |
| Threshing and Reaping the 'BinaryMatrix' | ThreshedBinaryMatrix ThreshedBinaryMatrix-class threshLGF |