plotCtHeatmap {HTqPCR} | R Documentation

## Heatmap of qPCR Ct values.

### Description

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

### Usage

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

### Arguments

`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.

### Details

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.

### Value

A plot is created on the current graphics device.

### Author(s)

Heidi Dvinge

### See Also

`heatmap.2`

### Examples

    # 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))

[Package HTqPCR version 1.42.0 Index]