CluMix: Clustering and Visualization of Mixed-Type Data

Provides utilities for clustering subjects and variables of mixed data types. Similarities between subjects are measured by Gower's general similarity coefficient with an extension of Podani for ordinal variables. Similarities between variables are assessed by combination of appropriate measures of association for different pairs of data types. Alternatively, variables can also be clustered by the 'ClustOfVar' approach. The main feature of the package is the generation of a mixed-data heatmap. For visualizing similarities between either subjects or variables, a heatmap of the corresponding distance matrix can be drawn. Associations between variables can be explored by a 'confounderPlot', which allows visual detection of possible confounding, collinear, or surrogate factors for some variables of primary interest. Distance matrices and dendrograms for subjects and variables can be derived and used for further visualizations and applications.

Author
M. Hummel, A. Kopp-Schneider
Date of publication
2016-06-03 18:47:22
Maintainer
Manuela Hummel <m.hummel@dkfz.de>
License
GPL (>= 2)
Version
1.1

View on CRAN

Man pages

association
Function to calculate a measure for association between two...
CluMix-package
\Sexpr[results=rd,stage=build]{tools:::Rd_package_title("CluMix")}
confounderPlot
Confounder Plot
dendro.subjects
Subjects dendrogram
dendro.variables
Variables dendrogram
distmap
Display similarity matrix
dist.subjects
Distance matrix for subjects
dist.variables
Distance matrix for variables
mixdata
Small example dataset with variables of different types
mix.heatmap
Heatmap for data with variables of mixed types
similarity.subjects
Similarity matrix for subjects
similarity.variables
Similarity matrix for variables

Files in this package

CluMix
CluMix/inst
CluMix/inst/doc
CluMix/inst/doc/CluMix.pdf
CluMix/inst/doc/CluMix.R
CluMix/inst/doc/CluMix.Rnw
CluMix/NAMESPACE
CluMix/NEWS
CluMix/data
CluMix/data/mixdata.rda
CluMix/R
CluMix/R/similarity.variables.R
CluMix/R/confounderPlot.R
CluMix/R/dendro.variables.R
CluMix/R/association.R
CluMix/R/distmap.R
CluMix/R/visualization.R
CluMix/R/dendro.subjects.R
CluMix/R/similarities.R
CluMix/R/mix.heatmap.R
CluMix/R/dist.subjects.R
CluMix/R/similarity.subjects.R
CluMix/R/zzz.R
CluMix/R/dist.variables.R
CluMix/vignettes
CluMix/vignettes/references.bib
CluMix/vignettes/CluMix.Rnw
CluMix/MD5
CluMix/build
CluMix/build/vignette.rds
CluMix/build/partial.rdb
CluMix/DESCRIPTION
CluMix/man
CluMix/man/similarity.variables.Rd
CluMix/man/association.Rd
CluMix/man/dendro.variables.Rd
CluMix/man/mix.heatmap.Rd
CluMix/man/similarity.subjects.Rd
CluMix/man/dist.subjects.Rd
CluMix/man/dendro.subjects.Rd
CluMix/man/confounderPlot.Rd
CluMix/man/dist.variables.Rd
CluMix/man/mixdata.Rd
CluMix/man/CluMix-package.Rd
CluMix/man/distmap.Rd