hclustWidget: shiny-oriented GUI for cluster or classifier exploration

In MLInterfaces: Uniform interfaces to R machine learning procedures for data in Bioconductor containers

Description

shiny-oriented GUI for cluster or classifier exploration

Usage

hclustWidget(mat, featureName = "feature", title =
                 paste0("hclustWidget for ", deparse(substitute(mat))),
                 minfeats = 2, auxdf = NULL)

mlearnWidget(eset, infmla)

Arguments

mat	matrix with feature vectors in rows
featureName	name to be used for control that asks for number of features to use
title	widget title
minfeats	lower bound on number of features to use
auxdf	data.frame with number of rows equal to nrow(mat), with metadata to be displayed in hovering tooltip
eset	instance of ExpressionSet-class
infmla	instance of formula, with dependent variable values obtained in pData(eset), and independent variable specified as "." or as properly munged elements of featureNames(eset).

Details

Experimental tool to illustrate impacts of choice of distance, agglomeration method, etc.

Value

a shinyApp result that will display in active browser

Note

mlearnWidget will attempt to nicely produce a variable importance plot using randomForestI. This means that the annotation package for probe identifiers should be loaded or an error will be thrown.

Author(s)

VJ Carey <[e-mail]>

Examples

# should run with example(hclustWidget, ask=FALSE)
if (interactive()) {
 library(shiny)
 library(MASS)
 data(crabs)
 cr = data.matrix(crabs[,-c(1:3)])
 au = crabs[,1:3]
 show(hclustWidget(cr, auxdf=au))
## must use stop widget button to proceed
  library(ALL)
  library(hgu95av2.db)
  data(ALL)
  show(mlearnWidget(ALL[1:500,], mol.biol~.))
 }

Example output

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

Loading required package: Biobase
Welcome to Bioconductor

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

Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: XML
Loading required package: cluster
Warning message:
replacing previous import 'BiocGenerics::var' by 'stats::var' when loading 'MLInterfaces' 
Warning message:
system call failed: Cannot allocate memory 

MLInterfaces documentation built on Nov. 8, 2020, 8:14 p.m.