plotCtScatter: Scatterplot of two sets of Ct values from qPCR data.

In HTqPCR: Automated analysis of high-throughput qPCR data

Description

Produces a plot of Ct values from two samples plotted against each other. Features can be marked based on for example feature class or type.

Usage

plotCtScatter(q, cards = c(1, 2), col = "class", pch = 20, diag = FALSE, cor = TRUE, Ct.max = 35, legend = TRUE, ...)

Arguments

q	object of class qPCRset.
cards	vector, the two cards to plot against each other.
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, the point type to use for the plot.
diag	logical, should the diagonal line y=x be plotted.
cor	logical, should information about the correlation between the two samples be included in the plot. The correlation is calculated both with and without removing Ct values above Ct.max.
Ct.max	numeric, all Ct values above this will be removed for calculating one of the correlations.
legend	logical, if col is either "type" or "class", should a colour legend for these be included.
...	any other arguments are passed to plot.

Value

A figure is generated in the current graphics device.

Author(s)

Heidi Dvinge

Examples

# Load example data
data(qPCRraw)
# Various types of plot
plotCtScatter(qPCRraw, cards=c(1,2))
plotCtScatter(qPCRraw, cards=c(1,4), col="type")
plotCtScatter(qPCRraw, cards=c(1,4), col="black", cor=FALSE, diag=TRUE)

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.