plotSmoothed: plotSmoothed

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/quantsmooth.R

Description

Plot a smoothed line together with the original data values

Usage

1
  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

1
2
	 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.