plotCtHeatmap: Heatmap of qPCR Ct values.
In HTqPCR: Automated analysis of high-throughput qPCR data

Description Usage Arguments Details Value Author(s) See Also Examples

Function for drawing a heatmap of Ct values from high-throughput qPCR experiments such as using TaqMan Low Density Arrays.

1	plotCtHeatmap(q, main = NULL, col, col.range, dist = "pearson", zero.center, mar, gene.names, sample.names, ...)

`q`	object of class qPCRset.
`main`	character string, plot title.
`col`	the colours to use. See details.
`col.range`	vector, the range of colours to use.
`dist`	character string, specifying whether to use "pearson" correlation (default) or "euclidean" distance for the clustering.
`zero.center`	logical, should the colours be shifted to be zero-centered. See details.
`mar`	vector, the size of the borrom and right hand side margins.
`gene.names`	character vector, names to replace the genes (rows) with. See details.
`sample.names`	character vector, names to replace the samples (columns) with. See details.
`...`	any other arguments will be passed to the `heatmap.2` function.

This function may be used to cluster the raw or normalized Ct values, and present the result in a heatmap.

The color range is used to represent the range of values for the statistic. If col==NULL the colour will be set to a spectrum from red to blue/purple, unless there are negative values in which case it goes red-yellow-green to reflect up and down regulation of genes. If zero.center=NULL then zero.center will automatically be set to TRUE to make the colour scale symmetric around 0.

Especially gene names will often not be readable in a standard size plotting device, and might therefore be removed. If gene.names or sample.names is set to a single character (such as "" for no naming), then this character will be repeated for all rows or columns.

A standard heatmap is drawn, but this can be modified extensively using the arguments available in the heatmap.2 function.

A plot is created on the current graphics device.

Heidi Dvinge

heatmap.2

# Load example data
data(qPCRraw)
# Some standard heatmaps
plotCtHeatmap(qPCRraw, gene.names="")
plotCtHeatmap(qPCRraw, gene.names="", dist="euclidean", col.range=c(10,35))
plotCtHeatmap(qPCRraw, gene.names="", dist="euclidean", col=colorRampPalette(rev(brewer.pal(9, "YlGnBu")))(20))

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