plotData: Plotting data

In jotsetung/GenomePlotR: Plotting data in genomic context

Description

This function is in principal identical to the plot and points, i.e. it either plots data points or adds them to an existing plot. Besides that the function also allows to transform/rescale the values and the coordinate system of the data in order to be able to plot e.g. data points with a range of values larger than available in an existing plot. X and y axis, if plotted, correspond always to the original data range of the submitted values.

Usage

plotData(x, y, add = FALSE, x.axis = !add, y.axis = !add, x.axis.side = 1, y.axis.side = 2, transform.range.x = NULL, original.range.x = range(x), original.range.y = range(y), transform.range.y = NULL, ylim, xlim, xlab = "x", ylab = "y", ...)

Arguments

x	Numerical vector with the values to plot. If not submitted a sequence from 1 to the length of y is used instead.
y	Numerical vector with the y-coordinates of the points.
add	If the data should be added to an existing plot.
x.axis	If a x-axis should be drawn (displaying the original, and not the transformed, data range).
y.axis	If a y-axis should be drawn (displaying the original, and not the transformed, data range).
x.axis.side	The side where the x axis should be added to the plot (1 bottom or 3 top).
y.axis.side	The side where the y axis should be added to the plot (2 left or 4 right side).
transform.range.x	Transform the x values that they fit into this new data range. Note: to add more then one set of data points the original.range.x argument should also be used (see the notes section as well as the examples below).
original.range.x	The original data range of the values from argument x.
original.range.y	The original data range of the values from argument y.
transform.range.y	Transform the y values that they fit into this new data range. Note: to add more then one set of data points to an existing plot, the original.range.x argument should also be used (see the notes and warnings section as well as the examples below).
ylim	Optionally define the limits on the y-axis.
xlim	Optionally define the limits on the x-axis.
xlab	Label for the x-axis. Defaults to x.
ylab	Label for the y-axis. Defaults to y.
...	Additional arguments to be passed to the plot or points function (like pch for point type, col for the color...).

Details

This function allows to add data points to an existing plot, also if the xlim and ylim of the plot would not allow to display the data.

Value

A plot.

Note

If more then one set of data points is added to a plot and the transform.range.x and transform.range.y arguments are used it is important to use also the original.range.x and original.range.y arguments to define the range of all data points that will be plotted, otherwise the individual sets of points are each scaled to the new range. See the examples section below for the correct and wrong usage of this function.

Author(s)

Johannes Rainer

See Also

transformTo, plotFeatures

Examples

## generate some random data to be plotted.
set.seed( 18011977 )
Y <- rnorm( 5 )
Y2 <- rnorm( 5 )

Y
Y2
## assume we want to plot this data into a plot with a range from 5-20 on the
##x and 2-10 on the y axis:
plotData( x=1:5, y=Y, transform.range.x=c( 5, 20 ), transform.range.y=c( 2, 10 ), original.range.y=range( c( Y, Y2 ) ) )
plotData( x=1:5, y=Y2, transform.range.x=c( 5, 20 ), transform.range.y=c( 2, 10 ), original.range.y=range( c( Y, Y2 ) ), add=TRUE, col="green" )
points( 20, 10, pch=15 )

## The code below should never be used to add data from more then one data vector
##into an existing plot using the transform.range.x and transform.range.y
## the function will always assign the smalles value in y to 2 and the largest
##to 10, unless we specifiy the range of all values we want to add to the plot
##by the argument original.range
plotData( x=1:5, y=Y, transform.range.x=c( 5, 20 ), transform.range.y=c( 2, 10 ) )
plotData( x=1:5, y=Y2, transform.range.x=c( 5, 20 ), transform.range.y=c( 2, 10 ), add=TRUE, col="red" )

## add data to an existing plot...
plot( 3, 3, pch=15, xlim=c( 2, 4 ), ylim=c( 2, 4 ) )
plotData( x=1:5, y=Y, transform.range.x=c( 3, 4 ), transform.range.y=c( 2.5, 4 ), add=TRUE, original.range.y=range( c( Y, Y2 ) ), y.axis=TRUE, y.axis.side=4 )
plotData( x=1:5, y=Y2, transform.range.x=c( 3, 4 ), transform.range.y=c( 2.5, 4 ), add=TRUE, original.range.y=range( c( Y, Y2 ) ), col="green" )

jotsetung/GenomePlotR documentation built on May 19, 2019, 9:41 p.m.