cluster_GO: Generates a hierarchical clustering of the samples

In kevinrue/GOexpress: Visualise microarray and RNAseq data using gene ontology annotations

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"
    )

kevinrue/GOexpress documentation built on May 19, 2020, 7:23 p.m.