plotCtBoxes: Boxplots for qPCR Ct values.

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

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

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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

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# 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 May 6, 2019, 2:28 a.m.