cluster_GO {GOexpress} | R Documentation

## Generates a hierarchical clustering of the samples

### Description

Clusters the samples using only the expression levels of genes associated with a given go_id.

### Usage

    cluster_GO(
        go_id, result, eSet, f=result$factor, subset=NULL,
        method_dist="euclidean", method_hclust="average", cex=0.8,
        main=paste(go_id, result$GO[result$GO$go_id == go_id, "name_1006"]),
        xlab="Distance", cex.main=1, main.Lsplit=NULL, ...)

### Arguments

`go_id` | A Gene Ontology (GO) identifier.
`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.
`f` | The grouping factor in `phenodata` to label the samples by.
`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).
`method_dist` | The method used to calculate distance between samples. See the `dist()` method from package `stats`.
`method_hclust` | The method used to cluster samples. See the `hclust()` method from package `stats`.
`cex` | A numeric value defining the character expansion of text in the plot.
`main` | A character string for the main title of the plot.
`xlab` | A label for the x axis, defaults to "Distance".
`cex.main` | Scaling factor of the main title font size. Default is 1. We suggest to use it in combination with the argument `main.Lsplit` for GO terms with long names.
`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 parameters passed on to `dist()`, `hclust()` and `plot()`.

### Value

Returns the output of the `plot()` function.

### Author(s)

Kevin Rue-Albrecht

### See Also

Method `GO_analyse`.

### Examples

    # load the sample output data
    data(AlvMac_results)

    # Hierarchical clustering of samples based on the same GO term
    cluster_GO(
        go_id="GO:0034142", result=AlvMac_results, eSet=AlvMac, cex=0.7
        )

    # Re-label sample by another factor
    cluster_GO(
        go_id="GO:0034142", result=AlvMac_results, eSet=AlvMac, cex=0.7, f="Group"
        )

[Package GOexpress version 1.28.0 Index]