plot.DNAmixture {DNAmixturesLite} | R Documentation |
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 class '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,
...
)
Arguments
x |
A |
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
|
dyecol |
List containing for each mixture a vector of dye
names. The default is to use the names in |
pw |
Peaks are |
threshold |
Should the detection thresholds be indicated on the plot? |
panel |
Alternative function for drawing the peaks. For
instance |
add |
Add to existing plot? (not meaningful if |
ask |
Should the user be prompted for page changes? The
default is |
... |
Other parameters to be passed on to |
Value
A data.frame
containing the plotted data points.
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))