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

Description Usage Arguments Value Author(s) Examples

View source: R/plotCtScatter.R

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

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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

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# 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 May 2, 2018, 2:08 a.m.