EnvioPlot: Visualize cluster's molecular entropy by violin plot

In HCsnip: Semi-supervised adaptive-height snipping of the Hierarchical Clustering tree

Description

This function first calculates the entopy of each sample in the given partition, and make a violin plot for each cluster. If clusters are different in term of their molecular profiles, then one may expect density differences in the violin plot.

Usage

EnvioPlot(X, method = "knn", parti, horizontal = FALSE, 
               col = NULL, names = NULL, ...)

Arguments

X	An object of class ExpressionSet or data matrix from which partition is obtained. Columns are assumed to represent samples, and rows represent sample's features. Missing values are allowed.
method	Type of method to calculate sample's molecular entropy. Either knn or normal.
parti	A partition for which violin plot to be made.
horizontal	Should boxes are organized horizontally? default is FALSE.
col	A vector of colors for each cluster. Should be equal the number of clusters in x.
names	A vector of labels for each cluster.
...	Arguments for hdEntropy to calculate the molecular entropy from the sigaR package.

Value

The entropy estimate is returned as a numeric.

Author(s)

Askar Obulkasim

References

van Wieringen,N.W. and van der Vaart,W.A. (2010) "Statistical analysis of the cancer cell's molecular entropy using high-throughput data", Bioinformatics, 27, 556-563.

Adler,D. (2005). vioplot: A violin plot is a combination of a box plot and a kernel density plot, R package, http://cran.r-project.org/web/packages/vioplot/index.html.

See Also

hdEntropy

Examples

data(BullingerLeukemia)
attach(BullingerLeukemia)
cl <- cutree(hclust(as.dist(1 - cor(em[, 1:60])), method = "ward"), k = 2)
result <- EnvioPlot(X = em[, 1:60], parti = cl)

Example output

Loading required package: survival
Loading required package: coin
Loading required package: fpc
Loading required package: clusterRepro
Loading required package: impute
Loading required package: randomForestSRC

 randomForestSRC 2.5.0 
 
 Type rfsrc.news() to see new features, changes, and bug fixes. 
 

Loading required package: sm
Package 'sm', version 2.2-5.4: type help(sm) for summary information
Loading required package: sigaR
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: CGHbase
Loading required package: marray
Loading required package: limma

Attaching package: 'limma'

The following object is masked from 'package:BiocGenerics':

    plotMA

Loading required package: mvtnorm
The "ward" method has been renamed to "ward.D"; note new "ward.D2"

HCsnip documentation built on Nov. 17, 2017, 11:17 a.m.