prepareParameters2: prepareParameters2

In karyoploteR: Plot customizable linear genomes displaying arbitrary data

Description

Prepare and normalize the parameters for functions with x and y parameters

Usage

prepareParameters2(function.name, karyoplot, data=NULL, chr=NULL, x=NULL, y=NULL, ymax=NULL, ymin=NULL, r0=NULL, r1=NULL, data.panel=1, filter.data=TRUE, ...)

Arguments

function.name	(character) The name of the function calling prepareParameters2. Only user for error reporting.
karyoplot	(KaryoPlot) A karyoplot object.
data	A GRanges. It can be NULL or a GRanges.
chr	A character representing the chromosome names.
x	The position in the chromosome in number of bases.
y	The value to be plotted.
ymax	The maximum value of y
ymin	The minimum value of y
r0	The start of the range to use for plotting
r1	The end of the range to use for plotting
data.panel	The data panel to use
filter.data	A boolean indicating if data should be filtered so only data in visible chromosomes is kept. (defaults to TRUE, filter data)
...	Any additional parameter

Details

This function prepares and normalizes the parameters for plotting functions with x and y parameters (as opposed to x0, x1, y0 and y1) so functions can offer a richer interface while internally dealing only with standard and simple code. It extracts the positions from data if available and applies the r0 and r1 scaling. It returns the ready to plot values in a list with only chr, x and y. Individual parameters (chr, x and y) take precedence over data. All parameters are interpreted and used as explained in kpPoints. It also filters out any data points corresponding to chromosomes not present in the current karyoplot.

Value

A list with three values: chr, x and y. Each of them a vector of the same length with the normalized values to plot.

Note

This function is only useful when creating custom plotting functions. It is not intended to the general user.

For detailed documentation on the parameters, see kpPoints

See Also

kpPoints

Examples

kp <- plotKaryotype()
prepareParameters2("TestFunc", kp, data=NULL, chr="chr1", x=c(10, 20, 30), y=c(0, 1, 2), r0=0, r1=0.5, ymin=0, ymax=2)

 

karyoploteR documentation built on Nov. 8, 2020, 5:52 p.m.