add_track.Rd
Add self-defined graphics track by track
add_track(gr = NULL, category = NULL, track = current_track() + 1, clip = TRUE, panel_fun = function(gr) NULL, panel.fun = NULL, use_raster = FALSE, raster_device = c("png", "jpeg", "tiff", "CairoPNG", "CairoJPEG", "CairoTIFF"), raster_quality = 1, raster_device_param = list())
gr | genomic regions. It should be a data frame in BED format or a |
---|---|
category | subset of categories (e.g. chromosomes) that users want to add graphics. The value can be a vector which contains more than one category. By default it is all available categories. |
track | which track the graphics will be added to. By default it is the next track. The value should only be a scalar. |
clip | whether graphics are restricted inside the cell. |
panel_fun | self-defined panel function to add graphics in each 'cell'. THe argument |
panel.fun | deprecated |
use_raster | whether render the each panel as a raster image. It helps to reduce file size when the file size is huge. |
raster_device | graphic device which is used to generate the raster image |
raster_quality | a value set to larger than 1 will improve the quality of the raster image. A temporary image with |
raster_device_param | a list of further parameters for the selected graphic device |
Initialization of the Trellis layout and adding graphics are two independent steps.
Once the layout initialization finished, each cell will be an independent plotting region.
As same as panel_fun
in circlize-package
, the self-defined function panel_fun
will be applied on every cell in the specified track (by default it is the 'current' track).
When adding graphics in each cell, get_cell_meta_data
can return several meta data for the current cell.
Since this package is implemented by the grid
graphic system, grid
-family functions
(such as grid.points
, grid.rect
, ...) should be used to add graphics. The usage
of grid
functions is quite similar as the traditional graphic functions.
Followings are several examples:
grid.points(x, y) grid.lines(x, y) grid.rect(x, y, width, height)
Graphical parameters are usually passed by gpar
:
grid.points(x, y, gp = gpar(col = "red") grid.rect(x, y, width, height, gp = gpar(fill = "black", col = "red"))
grid
system also support a large number of coordinate measurement systems by defining proper unit
object
which provides high flexibility to place graphics on the plotting regions.
grid.points(x, y, default.units = "npc") grid.rect(x, y, width = unit(1, "cm"))
You can refer to the documentations and vignettes of grid-package
to get a overview.
No value is returned.
There are several functions which draw specific graphics and are implemented by add_track
:
# There is no example NULL#> NULL