Package: Mercator 1.1.5
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_1.1.5.tar.gz
Mercator_1.1.5.tar.gz(r-4.5-noble)Mercator_1.1.5.tar.gz(r-4.4-noble)
Mercator_1.1.5.tgz(r-4.4-emscripten)Mercator_1.1.5.tgz(r-4.3-emscripten)
Mercator.pdf |Mercator.html✨
Mercator/json (API)
NEWS
# 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
- CML1000 - CML Cytogenetic Data
- CML500 - CML Cytogenetic Data
- fakeclin - CML Cytogenetic Data
- fakedata - CML Cytogenetic Data
- lgfFeatures - CML Cytogenetic Data
Last updated 1 months agofrom:31454f3f18. Checks:OK: 2. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Nov 22 2024 |
R-4.5-linux | OK | Nov 22 2024 |
Exports:addVisualizationbarplotbinaryDistanceBinaryMatrixdownsamplegetClustershistMercatorplotreclusterrecolorremapColorsremoveDuplicateFeaturesremoveDuplicatesscattersetClustersshowtthreshLGF
Dependencies:ade4askpassBiobaseBiocGenericschangepointClassDiscoverycliclueclustercolorspacecpmcpp11dendextendfansifarverflexmixgenericsggplot2gluegridExtragtablehereigraphisobandjsonlitekernlabKernSmoothkohonenlabelinglatticelifecyclemagrittrMASSMatrixmclustmgcvmodeltoolsmovMFmunsellnlmennetoompaBaseoompaDataopensslPCDimensionpillarpixmappkgconfigpngPolychromeR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenRcppTOMLreticulaterlangrprojrootRSpectraRtsnescalesscatterplot3dskmeansslamspsysThreshertibbleumaputf8vctrsviridisviridisLitewithrzoo
Mercator for Continuous Data
Rendered frommercVis.Rmd
usingknitr::rmarkdown
on Nov 22 2024.Last update: 2020-08-24
Started: 2020-08-24
UMAP and SOM from Distance Matrices
Rendered fromumap-som.Rmd
usingknitr::rmarkdown
on Nov 22 2024.Last update: 2021-07-16
Started: 2021-07-16
Using the Mercator Package
Rendered frommercator.Rmd
usingknitr::rmarkdown
on Nov 22 2024.Last update: 2021-01-10
Started: 2019-08-02
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 |