kpAddBaseNumbers {karyoploteR} | R Documentation |
Plots the base numbers along the chromosome ideograms
kpAddBaseNumbers(karyoplot, tick.dist=20000000, tick.len=5, add.units=FALSE, minor.ticks=TRUE, minor.tick.dist=5000000, minor.tick.len=2, cex=0.5, tick.col=NULL, minor.tick.col=NULL, clipping=TRUE, ...)
karyoplot |
(karyoplot object) A valid karyoplot object created by a call to |
tick.dist |
(numeric) The distance between the major numbered tick marks in bases |
tick.len |
(numeric) The length of the major tick marks in plot coordinates |
add.units |
(boolean) Add the units (Mb, Kb...) to the tick labels. Defaults to FALSE. |
minor.ticks |
(boolean) Whether to add unlabeled minor ticks between the major ticks |
minor.tick.dist |
(numeric) The distance between the minor ticks in bases |
minor.tick.len |
(numeric) The length of the minor tick marks in plot coordinates |
cex |
(numeric) The cex parameter for the major ticks label |
tick.col |
(color) If specified, the color to plot the major ticks. Otherwise the default color or, if given, the col parameter will be used. (Defaults to NULL) |
minor.tick.col |
(color) If specified, the color to plot the minor ticks. Otherwise the default color or, if given, the col parameter will be used. (Defaults to NULL) |
clipping |
(boolean) |
... |
Any other parameter to be passed to internal function calls. Specially useful for graphic parameters. |
This function can be used to add the base numbers scale to the chromosome ideograms. The base numbers and ticks witll be drawn next to the ideograms and not on a separate independent x axis. It is possible to control the number and position of the tick marks and labels
Returns the original karyoplot object, unchanged.
kp <- plotKaryotype() kpAddBaseNumbers(kp) kp <- plotKaryotype(chromosomes="chr17") kpAddBaseNumbers(kp, tick.dist=10000000, minor.tick.dist=1000000)