Usage
plotSmoothed(intensities, position, ylim=NULL, ylab="intensity", xlab="position", normalized.to=NULL, grid=NULL, smooth.lambda=2, interval=0.5, plotnew=TRUE, cols, cex.pts = 0.6, ...)
Arguments
intensities
numeric vector or matrix, data are plotted by column
position
numeric vector; the length should be the number of rows in intensities
ylim
numeric vector of length 2, limits for plot. If NULL then the minimal and maximal value in intensities is used
ylab
character, label for y-position
xlab
character, label for x-position
normalized.to
numeric, a line(s) is drawn at this horizontal position
grid
numeric, a line(s) is drawn at this vertical position
smooth.lambda
numeric, smoothing parameter see quantsmooth
interval
numeric (0..1), plotting of extra smoothed lines around median. With interval = 0.5 the 0.25 and 0.75 quartiles are plotted, with interval = 0.9 the 0.05 and 0.95 quantiles are plotted,
plotnew
logical, if TRUE a new plot is created, else the data are plotted into an existing plot
cols
color vector, colors for columns in intensities
cex.pts
size of the dots in the plot. Set to 0 to skip plotting the dots
...
extra parameters for plot