DNAmixturesLite (version 0.0-1)

plot.DNAmixture: Plot a DNA mixture model

Description

Plot of peak heights against repeat numbers for each marker.

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 DNAmixture
plot(
  x,
  traces = seq_len(x$ntraces),
  markers = x$markers,
  epg = FALSE,
  dyecol = lapply(dyes(x), names),
  pw = 0.4,
  threshold = TRUE,
  panel = NULL,
  add = FALSE,
  ask = NULL,
  ...
)

Value

A data.frame containing the plotted data points.

Arguments

x

A DNAmixture.

traces

Indices giving the mixtures, for which plots should be made.

markers

Vector of names giving the markers, for which plots should be made.

epg

Should a stylized EPG be produced? This requires a list of dyes to be specified for the mixtures, possibly through dyes.

dyecol

List containing for each mixture a vector of dye names. The default is to use the names in dyes(x). Set to NULL to ignore.

pw

Peaks are 2*pw wide.

threshold

Should the detection thresholds be indicated on the plot?

panel

Alternative function for drawing the peaks. For instance lines can be used for making triangular peaks. This functionality will be removed.

add

Add to existing plot? (not meaningful if EPG = TRUE.)

ask

Should the user be prompted for page changes? The default is TRUE, when the device is dev.interactive() and there is a need for multiple pages.

...

Other parameters to be passed on to plot

Examples

data(MC15, MC18, USCaucasian, SGMplusDyes)
mix <- DNAmixture(list(MC15, MC18), C = list(50,50), k = 3, K = c("K1", "K3"),
                  database = USCaucasian)
## Plot as a stylized EPG, using "orange" for the "yellow" dye
names(SGMplusDyes) <- c("blue", "green", "orange")
dyes(mix) <- list(SGMplusDyes, SGMplusDyes)
plot(mix, epg = TRUE)
## We can also supress the dye colors
plot(mix, traces = 1, epg = TRUE, dyecol = NULL)
## Create a user specified layout
op <- par(mfrow = c(2,3))
plot(mix, markers = c("VWA", "D19S433", "TH01"), col = "red")
par(mfrow = op)
plot(mix, traces = 1, markers = "D19S433", col = "orange",
     main = "A single marker", cex.main = 2, ylim = c(0,200))