plot_design {GOexpress} | R Documentation

## Plot Univariate Effects for genes associated with a Gene Ontology

### Description

Successively plots univariate effects of one or more `factors`, typically for a designed experiment as analyzed by `aov`().

### Usage

    plot_design(
        go_id, result, eSet, subset=NULL,
        factors=colnames(pData(eSet)), main="", main.Lsplit=NULL, ...)

### Arguments

`go_id` | A Gene Ontology (GO) identifier represented by at least one gene in the dataset.
`result` | The output of `GO_analyse()` or a subset of it obtained from `subset_scores()`.
`eSet` | `ExpressionSet` of the `Biobase` package including a gene-by-sample expression matrix in the `AssayData` slot, and a phenotypic information data-frame in the `phenodata` slot. In the expression matrix, row names are Ensembl gene identifiers or probeset identifiers, and column names are sample identifiers. In the phentypic data-frame, row names are sample idenfifiers, column names are grouping factors and phenotypic traits usable for the one-way ANOVA.
`subset` | A named list to subset `eSet`. Names must be column names existing in colnames(pData(eSet)). Values must be vectors of values existing in the corresponding column of pData(eSet).
`factors` | A set of column names from `phenodata`. Each of these values will be represented on the X-axis to investigate its effect on the average expression of a given genes for each level of that factor.
`main` | Changes the main title of the plots.
`main.Lsplit` | Number of characters after which a new-line character will be inserted in the main title. If this would occur within a word, the new-line character will be inserted before this word. Default is NULL, leaving the title on a single line.
`...` | Additional arguments which will be passed on to the `plot.design`() function.

### Value

The output of the `plot.design`() function.

### Author(s)

Kevin Rue-Albrecht

### See Also

Method `plot.design`.

### Examples

    # load the sample output data
    data(AlvMac_results)

    # Univariate plot
    plot_design(go_id="GO:0034142", eSet=AlvMac, result=AlvMac_results)

[Package GOexpress version 1.28.0 Index]