GOexpress (version 1.6.1)

heatmap_GO: Generates a heatmap and hierarchical clustering of the samples and the genes

Description

Clusters the samples and the genes associated with a GO term using the expression levels of genes related to a given ontology. Represents expression levels of those genes in a heatmap.

Usage

heatmap_GO( go_id, result, eSet, f=result$factor, subset=NULL, gene_names=TRUE, NA.names=FALSE, margins=c(7 ,5), scale="none", cexCol=1.2, cexRow=0.5,  labRow=NULL, cex.main=1, trace="none", expr.col=bluered(75),  row.col.palette="Accent", row.col=c(), main=paste( go_id, result$GO[result$GO$go_id == go_id,"name_1006"] ), 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).

gene_names

A boolean value. Default is TRUE, to label genes by their associated gene name. If FALSE, labels the genes by their feature identifier in the expression dataset (i.e. Ensembl gene identifier or microarray probeset).

NA.names

A boolean value. Default is TRUE. If labelling genes by their associated gene name (see argument gene_names), whether to display the gene feature identifier for gene features without associated gene name.

margins

A numeric vector of length 2 specifying the number of lines of margins to apply for the bottom and right margins, respectively. Defaults are 7 (bottom) and 5 (right). For Ensembl gene identifiers, we suggest setting manually a bottom margin of 13. See heatmap.2().

scale

Character indicating if the values should be centered and scaled in either the row direction or the column direction, or none. Default is "none". See heatmap.2().

cexCol, cexRow

Positive numbers, used as cex.axis in for the row or column axis labeling. Defaults are 1.2 and 1, respectively. See heatmap.2().

labRow

A character vector of names to re-label the rows (samples). If vector of length 1, it is assumed to be a column name in the phenoData slot. Default are the values of the factor f. See heatmap.2().

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.

trace

Character string indicating whether a solid "trace" line should be drawn across each 'row' or down each 'column', both' or 'none'. The distance of the line from the center of each color-cell is proportional to the size of the measurement. Defaults to 'none'.

expr.col

Character vector indicating the colors to represent the different levels of gene expression. Defaults to a colormap of 75 shades ranging from blue (low) to red (high) and centered around white. If using differential expression data, you should probably use greenred(75) instead.

row.col.palette

A valid RColorBrewer palette name to fetch the colormap from, to color-code the groups of samples.

row.col

A vector of color names or codes. The number of colors provided must match the number of levels of the grouping factor. Default to an palette of up to 9 colors marking the different levels of the predefined grouping factor on the left side of the heatmap.

main

Main title of the figure. Default is paste(go_id, go_name).

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 passed on to heatmap.2().

Value

Returns the output of the heatmap.2() function.

See Also

Method heatmap.2, GO_analyse, and brewer.pal.info.

Examples

# load the sample output data
data(AlvMac_results)

# Heatmap the top-ranked GO term (toll-like receptor 4 signaling pathway) as
# example
heatmap_GO(go_id="GO:0034142", result=AlvMac_results, eSet=AlvMac)

# Same with larger sample labels on the right hand side.
heatmap_GO(go_id="GO:0034142", result=AlvMac_results, eSet=AlvMac, cexRow=1)

# Change the color-coding to green-black-red gradient (more appropriate for
# differential expression values)
library(gplots)
heatmap_GO(
    go_id="GO:0034142", result=AlvMac_results, eSet=AlvMac,
    expr.col=greenred(75)
    )