Plot.all {GlobalAncova} | R Documentation

## Combined visualization of sequential decomposition and influence of single genes on the GlobalAncova statistic

### Description

Plot that combines `Plot.genes` and `Plot.sequential` into one graphic.

### Usage

    Plot.all(xx, formula, model.dat = NULL, test.genes = NULL, name.geneset = "")

### Arguments

`xx` | Matrix of gene expression data, where columns correspond to samples and rows to genes. The data should be properly normalized beforehand (and log- or otherwise transformed). Missing values are not allowed. Gene and sample names can be included as the row and column names of `xx`.
`formula` | Model formula for the linear model.
`model.dat` | Data frame that contains all the variable information for each sample.
`test.genes` | Vector of gene names or gene indices specifying a gene set.
`name.geneset` | Name of the plotted geneset.

### Note

This work was supported by the NGFN project 01 GR 0459, BMBF, Germany.

### Author(s)

Ramona Scheufele ramona.scheufele@charite.de
Reinhard Meister meister@tfh-berlin.de
Manuela Hummel hummel@ibe.med.uni-muenchen.de
Urlich Mansmann mansmann@ibe.med.uni-muenchen.de

### See Also

`Plot.genes`, `Plot.sequential`, `GlobalAncova.decomp`, `GlobalAncova`

### Examples

    data(vantVeer)
    data(phenodata)
    data(pathways)

    Plot.all(vantVeer, formula = ~ ERstatus + metastases + grade, model.dat = phenodata, test.genes = pathways[[3]], name.geneset = "cell cycle pathway")

[Package GlobalAncova version 3.4.0 Index]