Plot.sequential: Visualization of sequential decomposition

Description Usage Arguments Note Author(s) See Also Examples

View source: R/Plot.sequential.R

Description

Plot to show the sum of squares decomposition for each gene into parts according to all variables.

Usage

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Plot.sequential(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 m.hummel@dkfz.de
Urlich Mansmann mansmann@ibe.med.uni-muenchen.de

See Also

GlobalAncova.decomp, Plot.genes, GlobalAncova

Examples

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

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

hummelma/GlobalAncova documentation built on Feb. 4, 2021, 8:25 a.m.