Add self-defined graphics track by track

Description

Add self-defined graphics track by track

Usage

add_track(gr = NULL, category = NULL, track = current_track() + 1,
    clip = TRUE, panel_fun = function(gr) NULL, panel.fun = NULL)

Arguments

Details

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.

Value

No value is returned.

Author(s)

Zuguang Gu <z.gu@dkfz.de>

See Also

There are several functions which draw specific graphics and are implemented by add_track:

• add_points_track

• add_segments_track

• add_lines_track

• add_rect_track

• add_heatmap_track

Examples

require(circlize)
bed = circlize::generateRandomBed()
gtrellis_layout(track_ylim = range(bed[[4]]))
add_track(bed, panel.fun = function(bed) {
    x = (bed[[2]] + bed[[3]]) / 2
    y = bed[[4]]
    grid.points(x, y, pch = 16, size = unit(0.5, "mm"))
})

# you can add graphics in any cell by specifying `category` and `track`
all_chr = paste0("chr", 1:22)
letter = strsplit("MERRY CHRISTMAS!", "")[[1]]
gtrellis_layout(nrow = 5)
for(i in seq_along(letter)) {
    add_track(category = all_chr[i], track = 1, panel.fun = function(gr) {
        grid.text(letter[i], gp = gpar(fontsize = 30))
    })
}

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(gtrellis)
Loading required package: grid
Loading required package: IRanges
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/gtrellis/add_track.rd_%03d_medium.png", width=480, height=480)
> ### Name: add_track
> ### Title: Add self-defined graphics track by track
> ### Aliases: add_track
> 
> ### ** Examples
> 
> require(circlize)
Loading required package: circlize
> bed = circlize::generateRandomBed()
> gtrellis_layout(track_ylim = range(bed[[4]]))
> add_track(bed, panel.fun = function(bed) {
+     x = (bed[[2]] + bed[[3]]) / 2
+     y = bed[[4]]
+     grid.points(x, y, pch = 16, size = unit(0.5, "mm"))
+ })
Warning message:
In add_track(bed, panel.fun = function(bed) { :
  `panel.fun` is deprecated, please use `panel_fun`.
> 
> # you can add graphics in any cell by specifying `category` and `track`
> all_chr = paste0("chr", 1:22)
> letter = strsplit("MERRY CHRISTMAS!", "")[[1]]
> gtrellis_layout(nrow = 5)
> for(i in seq_along(letter)) {
+     add_track(category = all_chr[i], track = 1, panel.fun = function(gr) {
+         grid.text(letter[i], gp = gpar(fontsize = 30))
+     })
+ }
There were 16 warnings (use warnings() to see them)
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>