plotSmoothed {quantsmooth}R Documentation

plotSmoothed

Description

Plot a smoothed line together with the original data values

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

Details

This function plots the raw data values as dots and the median smoothed values as a continuous line. If interval is supplied these are plotted as lines in different line types. More than 1 interval can be given.

Value

This function is used for its side effects

Author(s)

Jan Oosting

See Also

quantsmooth

Examples

         data(chr14)
         plotSmoothed(bac.cn,bac.pos,ylim=c(1,2.5),normalized.to=2,smooth.lambda=2.5)

[Package quantsmooth version 1.4.0 Index]