plotCtBoxes: Boxplots for qPCR Ct values.

In HTqPCR: Automated analysis of high-throughput qPCR data

Description

Function for making boxplots of Ct values from high-throughput qPCR data. The boxes can be made either using all values on each card, or stratified by different feature information.

Usage

plotCtBoxes(q, cards = TRUE, xlab = "", col, main = NULL, names, stratify = "type", mar = c(7, 4, 3, 1), ...)

Arguments

q	object of class qPCRset.
cards	vector, the numbers of the cards to plot. Defaults to TRUE = all cards.
xlab	character string, label for the x-axis.
col	vector of colours to use, defaults to different colour for each card.
main	character string, plot title.
names	vector, names to plot under the boxes. Defaults to sample names.
stratify	character, specifying what to stratify the Ct values by. NULL, the default means no stratification, "type" is the feature types of the qPCRset, and "class" the feature class.
mar	vector, the size of the margins. See par for details.
...	any other arguments will be passed to the boxplot or parfunction.

Details

For the stratified plots all boxes with Ct values from the same card are plotted in identical colours. "type" and "class" are automatically extracted from the qPCRset using featureType and featureClass.

Value

A plot is created on the current graphics device.

Author(s)

Heidi Dvinge

See Also

boxplot

Examples

# Loading the data
data(qPCRraw)
# Make plot with all samples or just a few
plotCtBoxes(qPCRraw, stratify=NULL)
plotCtBoxes(qPCRraw, cards=c(1,4))
plotCtBoxes(qPCRraw, stratify="class")

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. 8, 2020, 6:51 p.m.