plotCtPairs: Pairwise scatterplot of multiple sets of Ct values from qPCR...

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

View source: R/plotCtPairs.R

Description

Produces a plot of high-throughput qPCR Ct values from N number of samples plotted pairwise against each other in an N by N plot. The Ct values will be in the upper triangle, and the correlation between samples in the lower. Features can be marked based on for example feature class or type.

Usage

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plotCtPairs(q, cards = TRUE, lower.panel = panel.Ct.cor, upper.panel = panel.Ct.scatter, Ct.max = 35, col = "type", pch = 20, cex.cor = 2, cex.pch = 1, diag = TRUE, ...)

Arguments

q

object of class qPCRset.

cards

vector, the cards to plot against each other.

lower.panel

function, to use for plotting the lower triangle.

upper.panel

function, to use for plotting the upper triangle.

Ct.max

numeric, Ct values above this limit will be excluded when calculating the correlation.

col

vector with the colour(s) to use for the points, or a character string ("type" or "class") indicating whether points should be coloured according to featureType or featureClass of q.

pch

integer or single character, which plotting symbol to use for the points.

cex.cor

numeric, the expansion factor for the text in panel.Ct.cor.

cex.pch

numeric, the expansion factor for the points in panel.Ct.scatter.

diag

logical, should the diagonal line y=x be plotted.

...

any other arguments are passed to the panel function or pairs.

Details

Per default, the lower panels contain the correlations between data sets. For each correlation all complete pairs are used, i.e. NAs are ignored. If there are no complete observations between two samples the correlation will be set to NA.

Value

A figure is generated in the current graphics device.

Author(s)

Heidi Dvinge

See Also

pairs or plotCtScatter for plotting just two samples.

Examples

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# Load example data
data(qPCRraw)
# Various types of plot
plotCtPairs(qPCRraw, cards=1:4)
plotCtPairs(qPCRraw, col="black")
plotCtPairs(qPCRraw, Ct.max=40)

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.