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:Kevin R. Coombes [aut, cre], Caitlin E. Coombes [aut]

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

Datasets:

CML1000 - CML Cytogenetic Data
CML500 - CML Cytogenetic Data
fakeclin - CML Cytogenetic Data
fakedata - CML Cytogenetic Data
lgfFeatures - CML Cytogenetic Data

clustering

4.33 score 1 packages 12 scripts 642 downloads 347 mentions 19 exports 76 dependencies

Last updated 26 days agofrom:31454f3f18. Checks:OK: 2. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 23 2024
R-4.5-linux	OK	Oct 23 2024

Exports:addVisualization barplot binaryDistance BinaryMatrix downsample getClusters hist Mercator plot recluster recolor remapColors removeDuplicateFeatures removeDuplicates scatter setClusters show t threshLGF

Dependencies:ade4 askpass Biobase BiocGenerics changepoint ClassDiscovery cli clue cluster colorspace cpm cpp11 dendextend fansi farver flexmix ggplot2 glue gridExtra gtable here igraph isoband jsonlite kernlab KernSmooth kohonen labeling lattice lifecycle magrittr MASS Matrix mclust mgcv modeltools movMF munsell nlme nnet oompaBase oompaData openssl PCDimension pillar pixmap pkgconfig png Polychrome R6 rappdirs RColorBrewer Rcpp RcppArmadillo RcppEigen RcppTOML reticulate rlang rprojroot RSpectra Rtsne scales scatterplot3d skmeans slam sp sys Thresher tibble umap utf8 vctrs viridis viridisLite withr zoo

Mercator for Continuous Data

C.E. Coombes, Zachary B. Abrams, Kevin R. Coombes

Rendered frommercVis.Rmdusingknitr::rmarkdownon Oct 23 2024.

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

UMAP and SOM from Distance Matrices

C.E. Coombes, Zachary B. Abrams, Kevin R. Coombes

Rendered fromumap-som.Rmdusingknitr::rmarkdownon Oct 23 2024.

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

Using the Mercator Package

C.E. Coombes, Zachary B. Abrams, Suli Li, Kevin R. Coombes

Rendered frommercator.Rmdusingknitr::rmarkdownon Oct 23 2024.

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

Citation

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