plotCtHeatmap: Heatmap of qPCR Ct values.

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

View source: R/plotCtHeatmap.R

Description

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

Usage

1
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

1
2
3
4
5
6
# 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))

Example output

Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: RColorBrewer
Loading required package: limma

Attaching package: 'limma'

The following object is masked from 'package:BiocGenerics':

    plotMA

Warning message:
In read.dcf(con) :
  URL 'http://bioconductor.org/BiocInstaller.dcf': status was 'Couldn't resolve host name'

HTqPCR documentation built on Nov. 1, 2018, 2:23 a.m.