Produces a line plot showing the feature abundances across the fractions.
plotDist(
object,
markers,
fcol = NULL,
mcol = "steelblue",
pcol = getUnknowncol(),
alpha = 0.3,
type = "b",
lty = 1,
fractions = sampleNames(object),
ylab = "Intensity",
xlab = "Fractions",
ylim,
...
)
An instance of class MSnSet
.
A character
, numeric
or
logical
of appropriate length and or content used to
subset object
and define the organelle markers.
Feature meta-data label (fData column name) defining
the groups to be differentiated using different colours. If
NULL
(default) ignored and mcol
and pcol
are used.
A character
define the colour of the marker
features. Default is "steelblue"
.
A character
define the colour of the
non-markers features. Default is the colour used for features
of unknown localisation, as returned by
getUnknowncol
.
A numeric defining the alpha channel (transparency)
of the points, where 0 <= alpha <= 1
, 0 and 1 being
completely transparent and opaque.
Character string defining the type of lines. For
example "p"
for points, "l"
for lines,
"b"
for both. See plot
for all possible types.
Vector of line types for the marker profiles. Default
is 1 (solid). See par
for details.
A character
defining the phenoData
variable to be used to label the fraction along the x
axis. Default is to use sampleNames(object)
.
y-axis label. Default is "Intensity".
x-axis label. Default is "Fractions".
A numeric vector of length 2, giving the y coordinates range.
Additional parameters passed to plot
.
Used for its side effect of producing a feature distribution plot. Invisibly returns the data matrix.
library("pRolocdata")
data(tan2009r1)
j <- which(fData(tan2009r1)$markers == "mitochondrion")
i <- which(fData(tan2009r1)$PLSDA == "mitochondrion")
plotDist(tan2009r1[i, ], markers = featureNames(tan2009r1)[j])
plotDist(tan2009r1[i, ], markers = featureNames(tan2009r1)[j],
fractions = "Fractions")
## plot and colour all marker profiles
tanmrk <- markerMSnSet(tan2009r1)
plotDist(tanmrk, fcol = "markers")