Package: Mercator 1.1.4

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:Kevin R. Coombes, Caitlin E. Coombes

Mercator_1.1.4.tar.gz
Mercator_1.1.4.tar.gz(r-4.5-noble)Mercator_1.1.4.tar.gz(r-4.4-noble)
Mercator_1.1.4.tgz(r-4.4-emscripten)Mercator_1.1.4.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'))

Peer review:

Bug tracker:https://r-forge.r-project.org/projects/oompa

Datasets:

18 exports 0.00 score 76 dependencies

Last updated 2 months agofrom:a0c8d67fda58abb51b95709f29a26c7a42b52218

Exports:addVisualizationbarplotbinaryDistanceBinaryMatrixdownsamplegetClustersMercatorplotreclusterrecolorremapColorsremoveDuplicateFeaturesremoveDuplicatesscattersetClustersshowtthreshLGF

Dependencies:ade4askpassBiobaseBiocGenericschangepointClassDiscoverycliclueclustercolorspacecpmcpp11dendextendfansifarverflexmixggplot2gluegridExtragtablehereigraphisobandjsonlitekernlabKernSmoothkohonenlabelinglatticelifecyclemagrittrMASSMatrixmclustmgcvmodeltoolsmovMFmunsellnlmennetoompaBaseoompaDataopensslPCDimensionpillarpixmappkgconfigpngPolychromeR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenRcppTOMLreticulaterlangrprojrootRSpectraRtsnescalesscatterplot3dskmeansslamspsysThreshertibbleumaputf8vctrsviridisviridisLitewithrzoo

Mercator for Continuous Data

Rendered frommercVis.Rmdusingknitr::rmarkdownon May 29 2024.

Last update: 2020-08-24
Started: 2020-08-24

UMAP and SOM from Distance Matrices

Rendered fromumap-som.Rmdusingknitr::rmarkdownon May 29 2024.

Last update: 2021-07-16
Started: 2021-07-16

Using the Mercator Package

Rendered frommercator.Rmdusingknitr::rmarkdownon May 29 2024.

Last update: 2021-01-10
Started: 2019-08-02

Readme and manuals

Help Manual

Help pageTopics
Binary Distance Definitions Across MethodsbinaryDistance 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 iGraphdownsample
The 'Mercator' Distance Visualization ObjectaddVisualization 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 DataCML1000 CML500 fakeclin fakedata lgfFeatures mercator-data
Remove Duplicate Features or Samples from a Binary Matrix ObjectremoveDuplicateFeatures removeDuplicates
Changing Cluster and Color Assignments in Mercatorrecluster recolor remapColors setClusters
Threshing and Reaping the 'BinaryMatrix'ThreshedBinaryMatrix ThreshedBinaryMatrix-class threshLGF