plotDensOneAnnotInAllComp: Tests if groups of samples are differently distributed on the...
In MineICA: Analysis of an ICA decomposition obtained on genomics data

Description Usage Arguments Details Value Author(s) See Also Examples

Given a variable of the phenotype data (i.e vector of sample annotations), this function tests if the groups of samples formed by this variable are differently distributed on the components, in terms of contribution values. The distribution of the groups on the components are represented using density plots. It is possible to restrict the tests and the plots to a subset of samples and/or components.

  plotDensOneAnnotInAllComp(icaSet, keepVar, path = NULL,
    samples, keepComp, keepLev = NULL, colours = NULL,
    legend.title = NULL, doPlot = TRUE, cutoff = 0.05,
    onlySign = TRUE, resTests)

`icaSet`	an object of class `IcaSet`
`keepVar`	a variable label, i.e the label of a column of the pheno data of icaSet available in (`varLabels(icaSet)`) wich contains the groups of interest
`path`	the directory where the plots will be located
`samples`	a subset of sample names available in `samplenames(icaSet)`, if NULL (default) all samples are used
`keepComp`	a subset of components available in `indComp(icaSet)`, if NULL (default) all components are used
`keepLev`	the groups of interest, i.e the levels of the annotation `keepVar` to be considered
`colours`	A vector of colours indexed by the elements of `keepLev`, if NULL the colours are generated automatically using annot2Color
`legend.title`	title of the legend
`cutoff`	The threshold p-value for statistical significance
`doPlot`	if TRUE (default), the plots are drawn, else if FALSE only test results are returned
`onlySign`	if TRUE (default), only the significant results are plotted
`resTests`	a vector of p-values per component, if NULL (default) the p-values are calculated using Wilcoxon or Kruskal-Wallis test

Wilcoxon or Kruskal-Wallis tests are applied depending on the number of groups of interest from the considered annotation (argument keepLev). The plots are saved in individual files (one file per component) in arg 'path' if specified or in the current directory if not specificied. Ech individual file is nameb 'index-of-component_colAnnot.png.' Recall that the sample-contribution values are contained in A(icaSet), and the sample annotations in pData(icaSet).

One png image is created by plot and located in path. Each image is named by 'index-of-component_keepVar.png'.

Returns a data.frame of dimensions 'components x 1' containing the results of the non-parametric tests (Wilcoxon or Kruskal-Wallis tests) that test if the groups of interest are differently distributed on the components

Anne Biton

wilcoxOrKruskalOnA, codewriteHtmlResTestsByAnnot, codewilcox.test, codekruskal.test

## Not run: 
## load an example of IcaSet
data(icaSetCarbayo)

## have a look at the sample annotations which are available
varLabels(icaSetCarbayo)

## with doPlot=TRUE trace the contributions of the samples according
## to their grade on the components
restests <- plotDensOneAnnotInAllComp(icaSet=icaSetCarbayo, keepVar="GRADE",
                                                doPlot=FALSE)

## End(Not run)