plotSmoothed: plotSmoothed

In quantsmooth: Quantile smoothing and genomic visualization of array data

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)

quantsmooth documentation built on Nov. 8, 2020, 8:27 p.m.