View source: R/prepareParameters4.R
prepareParameters4 | R Documentation |
Prepare and normalize the parameters for functions with x0, x1 and y0, y1 parameters
prepareParameters4(function.name, karyoplot, data=NULL, chr=NULL, x0=NULL, x1=NULL, y0=NULL, y1=NULL, ymax=NULL, ymin=NULL, r0=NULL, r1=NULL, data.panel=1, filter.data=TRUE, ...)
function.name |
(character) The name of the function calling |
karyoplot |
(KaryoPlot) A karyoplot object. |
data |
A GRanges |
chr |
A character representing the chromosome names. |
x0 |
The position in the chromosome in number of bases. |
x1 |
The position in the chromosome in number of bases. |
y0 |
The value to be plotted. |
y1 |
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 |
This function prepares and normalizes the parameters for plotting functions
with x0, x1, y0 and y1 parameters (as opposed to x and y) 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
, x0
, x1
, y0
and y1
.
Individual parameters (chr
, x0
, x1
, y0
and
All parameters are interpreted and used as explained in kpRect
.
It also filters out any data points corresponding to chromosomes not present
in the current karyoplot.
A list with five values: chr
, x0
, x1
, y0
and y1
. Each of them
a vector of the same length with the normalized values to plot.
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 kpRect
kpRect
kp <- plotKaryotype()
prepareParameters4("TestFunc", kp, data=NULL, chr="chr1", x0=c(10, 20, 30), x1=c(20, 30, 40), y0=c(0, 1, 2), y1=c(0.5, 1.5, 3), r0=0, r1=0.5, ymin=0, ymax=3)
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