boxplot.DNAmixture {DNAmixturesLite}

Plot simulated peak heights for multiple DNA mixtures.

Description

A plot will be made for each combination of samples and markers specified, and it is up to the user to specify a layout for the plots (e.g. via calls to par)

IMPORTANT: This is the DNAmixturesLite package, which is intended as a service to enable users to try DNAmixtures without purchasing a commercial licence for Hugin. When at all possible, we strongly recommend the use of DNAmixtures rather than this lite-version. See https://dnamixtures.r-forge.r-project.org/ for details on both packages.

While the lite-version seeks to provide the full functionality of DNAmixtures, note that computations are much less efficient and that there are some differences in available functionality. Be aware that the present documentation is copied from DNAmixtures and thus may not accurately describe the implementation of this lite-version.

Usage

## S3 method for class 'DNAmixture'
boxplot(
  x,
  sims,
  traces = 1:x$ntraces,
  markers = x$markers,
  pw = 0.4,
  ylim = NULL,
  border = "grey",
  ...
)

Arguments

x

A DNAmixture.

sims

A set of simulated peak heights. See also rPeakHeight.

traces

Selected traces to plot.

markers

Selected markers to plot.

pw

Peaks are 2*pw wide.

ylim

Range of the y-axis.

border

Color of the boxes.

...

Arguments passed on to plot.DNAmixture.

Value

Invisibly the peak heights as used for the boxplots.

Author(s)

Therese Graversen

Examples

data(MC15, MC18, USCaucasian)
mix <- DNAmixture(list(MC15, MC18), C = list(50, 38), k = 3, K = c("K1", "K3"),
                  database = USCaucasian)
p <- mixpar(rho = list(30, 30), eta = list(30, 30), xi = c(0.08,0.08),
            phi = list(c(U1 = 0.1, K3 = 0.2, K1 = 0.7), c(K1 = 0.9, K3 = 0.05, U1 = 0.05)))
rpm <- rPeakHeight(mix, p, nsim = 1000, dist = "joint")
oldpar <- par("mfrow")
par(mfrow = c(1,2))
boxplot(mix, rpm, traces = 1:2, markers = "VWA")
par(mfrow = oldpar)


data(MC15, MC18, USCaucasian)
mix <- DNAmixture(list(MC15, MC18), C = list(50, 38), k = 3, K = "K3", database = USCaucasian)
p <- mixpar(rho = list(30, 30), eta = list(30, 30), xi = c(0.08,0.08),
            phi = list(c(U2 = 0.1, K3 = 0.2, U1 = 0.7), c(U1 = 0.9, K3 = 0.05, U2 = 0.05)))
rpm <- rPeakHeight(mix, p, nsim = 50, dist = "joint")
rpc <- rPeakHeight(mix, p, nsim = 50, dist = "conditional")
oldpar <- par("mfrow")
par(mfrow = c(2,2))
boxplot(mix, rpm, traces = 1:2, markers = "VWA") ## First row of plots
boxplot(mix, rpc, traces = 1:2, markers = "VWA") ## Second row of plots
par(mfrow = oldpar)
mixK <- DNAmixture(list(MC15, MC18), C = list(50, 38), k = 3, K = c("K1", "K2", "K3"),
                    database = USCaucasian)
pK <- mixpar(rho = list(30, 30), eta = list(30, 30), xi = list(0.08,0.08),
             phi = list(c(K2 = 0.1, K3 = 0.2, K1 = 0.7), c(K2 = 0.1, K3 = 0.2, K1 = 0.7)))
rpmK <- rPeakHeight(mixK, pK, nsim = 1000, markers = "D2S1338")
oldpar <- par(mfrow = c(1,2))
boxplot(mixK, rpmK, markers = "D2S1338")
par(oldpar)