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Last data update: 2014.03.03

R: Get meta data in a cell

get_cell_meta_data

R Documentation

Get meta data in a cell

Description

Get meta data in a cell

Usage

get_cell_meta_data(name, category, track)

Arguments

`name`	name of the supported meta data, see 'details' section.
`category`	which category. By default it is the current category.
`track`	which track. By default it is the current track.

Details

Following meta data can be retrieved:

name: name of the category.
xlim: xlim without including padding. Cells in the same column share the same xlim.
ylim: ylim without including padding.
extended_xlim: xlim with padding.
extended_ylim: ylim with padding.
original_xlim: xlim in original data.
original_ylim: ylim in original data.
column: which column in the layout.
row: which row in the layout.
track: which track in the layout.

The vignette has a graphical explanation of all these meta data.

Value

Corresponding meta data that user queried.

Author(s)

Zuguang Gu <z.gu@dkfz.de>

Examples

gtrellis_layout(ncol = 4, n_track = 3)
add_track(panel.fun = function(gr) {
    print(get_cell_meta_data("xlim"))
    print(get_cell_meta_data("ylim"))
    print(get_cell_meta_data("extended_xlim"))
    print(get_cell_meta_data("extended_ylim"))
    print(get_cell_meta_data("original_xlim"))
    print(get_cell_meta_data("original_ylim"))
    print(get_cell_meta_data("name"))
    print(get_cell_meta_data("column"))
    print(get_cell_meta_data("row"))
    print(get_cell_meta_data("track"))
    cat("\n\n")
})

for(chr in paste0("chr", 1:22)) {
    print(get_cell_meta_data("xlim", category = chr, track = 1))
    print(get_cell_meta_data("ylim", category = chr, track = 1))
    print(get_cell_meta_data("extended_xlim", category = chr, track = 1))
    print(get_cell_meta_data("extended_ylim", category = chr, track = 1))
    print(get_cell_meta_data("original_xlim", category = chr, track = 1))
    print(get_cell_meta_data("original_ylim", category = chr, track = 1))
    print(get_cell_meta_data("name", category = chr, track = 1))
    print(get_cell_meta_data("column", category = chr, track = 1))
    print(get_cell_meta_data("row", category = chr, track = 1))
    print(get_cell_meta_data("track", category = chr, track = 1))
    cat("\n\n")
}

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/get_cell_meta_data.rd_%03d_medium.png", width=480, height=480)
> ### Name: get_cell_meta_data
> ### Title: Get meta data in a cell
> ### Aliases: get_cell_meta_data
> 
> ### ** Examples
> 
> gtrellis_layout(ncol = 4, n_track = 3)
> add_track(panel.fun = function(gr) {
+     print(get_cell_meta_data("xlim"))
+     print(get_cell_meta_data("ylim"))
+     print(get_cell_meta_data("extended_xlim"))
+     print(get_cell_meta_data("extended_ylim"))
+     print(get_cell_meta_data("original_xlim"))
+     print(get_cell_meta_data("original_ylim"))
+     print(get_cell_meta_data("name"))
+     print(get_cell_meta_data("column"))
+     print(get_cell_meta_data("row"))
+     print(get_cell_meta_data("track"))
+     cat("\n\n")
+ })
xlim_start   xlim_end 
         0  249250621 
[1] 0 1
xlim_start   xlim_end 
         0  249250621 
[1] 0 1
    start       end 
        0 249250621 
[1] 0 1
[1] "chr1"
[1] 1
1 
1 
[1] 1


xlim_start   xlim_end 
         0  243199373 
[1] 0 1
xlim_start   xlim_end 
         0  243199373 
[1] 0 1
    start       end 
        0 243199373 
[1] 0 1
[1] "chr2"
[1] 2
1 
1 
[1] 1


xlim_start   xlim_end 
         0  198022430 
[1] 0 1
xlim_start   xlim_end 
         0  198022430 
[1] 0 1
    start       end 
        0 198022430 
[1] 0 1
[1] "chr3"
[1] 3
1 
1 
[1] 1


xlim_start   xlim_end 
         0  191154276 
[1] 0 1
xlim_start   xlim_end 
         0  191154276 
[1] 0 1
    start       end 
        0 191154276 
[1] 0 1
[1] "chr4"
[1] 4
1 
1 
[1] 1


xlim_start   xlim_end 
         0  249250621 
[1] 0 1
xlim_start   xlim_end 
         0  249250621 
[1] 0 1
    start       end 
        0 180915260 
[1] 0 1
[1] "chr5"
[1] 1
2 
2 
[1] 1


xlim_start   xlim_end 
         0  243199373 
[1] 0 1
xlim_start   xlim_end 
         0  243199373 
[1] 0 1
    start       end 
        0 171115067 
[1] 0 1
[1] "chr6"
[1] 2
2 
2 
[1] 1


xlim_start   xlim_end 
         0  198022430 
[1] 0 1
xlim_start   xlim_end 
         0  198022430 
[1] 0 1
    start       end 
        0 159138663 
[1] 0 1
[1] "chr7"
[1] 3
2 
2 
[1] 1


xlim_start   xlim_end 
         0  191154276 
[1] 0 1
xlim_start   xlim_end 
         0  191154276 
[1] 0 1
    start       end 
        0 146364022 
[1] 0 1
[1] "chr8"
[1] 4
2 
2 
[1] 1


xlim_start   xlim_end 
         0  249250621 
[1] 0 1
xlim_start   xlim_end 
         0  249250621 
[1] 0 1
    start       end 
        0 141213431 
[1] 0 1
[1] "chr9"
[1] 1
3 
3 
[1] 1


xlim_start   xlim_end 
         0  243199373 
[1] 0 1
xlim_start   xlim_end 
         0  243199373 
[1] 0 1
    start       end 
        0 135534747 
[1] 0 1
[1] "chr10"
[1] 2
3 
3 
[1] 1


xlim_start   xlim_end 
         0  198022430 
[1] 0 1
xlim_start   xlim_end 
         0  198022430 
[1] 0 1
    start       end 
        0 135006516 
[1] 0 1
[1] "chr11"
[1] 3
3 
3 
[1] 1


xlim_start   xlim_end 
         0  191154276 
[1] 0 1
xlim_start   xlim_end 
         0  191154276 
[1] 0 1
    start       end 
        0 133851895 
[1] 0 1
[1] "chr12"
[1] 4
3 
3 
[1] 1


xlim_start   xlim_end 
         0  249250621 
[1] 0 1
xlim_start   xlim_end 
         0  249250621 
[1] 0 1
    start       end 
        0 115169878 
[1] 0 1
[1] "chr13"
[1] 1
4 
4 
[1] 1


xlim_start   xlim_end 
         0  243199373 
[1] 0 1
xlim_start   xlim_end 
         0  243199373 
[1] 0 1
    start       end 
        0 107349540 
[1] 0 1
[1] "chr14"
[1] 2
4 
4 
[1] 1


xlim_start   xlim_end 
         0  198022430 
[1] 0 1
xlim_start   xlim_end 
         0  198022430 
[1] 0 1
    start       end 
        0 102531392 
[1] 0 1
[1] "chr15"
[1] 3
4 
4 
[1] 1


xlim_start   xlim_end 
         0  191154276 
[1] 0 1
xlim_start   xlim_end 
         0  191154276 
[1] 0 1
   start      end 
       0 90354753 
[1] 0 1
[1] "chr16"
[1] 4
4 
4 
[1] 1


xlim_start   xlim_end 
         0  249250621 
[1] 0 1
xlim_start   xlim_end 
         0  249250621 
[1] 0 1
   start      end 
       0 81195210 
[1] 0 1
[1] "chr17"
[1] 1
5 
5 
[1] 1


xlim_start   xlim_end 
         0  243199373 
[1] 0 1
xlim_start   xlim_end 
         0  243199373 
[1] 0 1
   start      end 
       0 78077248 
[1] 0 1
[1] "chr18"
[1] 2
5 
5 
[1] 1


xlim_start   xlim_end 
         0  198022430 
[1] 0 1
xlim_start   xlim_end 
         0  198022430 
[1] 0 1
   start      end 
       0 59128983 
[1] 0 1
[1] "chr19"
[1] 3
5 
5 
[1] 1


xlim_start   xlim_end 
         0  191154276 
[1] 0 1
xlim_start   xlim_end 
         0  191154276 
[1] 0 1
   start      end 
       0 63025520 
[1] 0 1
[1] "chr20"
[1] 4
5 
5 
[1] 1


xlim_start   xlim_end 
         0  249250621 
[1] 0 1
xlim_start   xlim_end 
         0  249250621 
[1] 0 1
   start      end 
       0 48129895 
[1] 0 1
[1] "chr21"
[1] 1
6 
6 
[1] 1


xlim_start   xlim_end 
         0  243199373 
[1] 0 1
xlim_start   xlim_end 
         0  243199373 
[1] 0 1
   start      end 
       0 51304566 
[1] 0 1
[1] "chr22"
[1] 2
6 
6 
[1] 1


xlim_start   xlim_end 
         0  198022430 
[1] 0 1
xlim_start   xlim_end 
         0  198022430 
[1] 0 1
    start       end 
        0 155270560 
[1] 0 1
[1] "chrX"
[1] 3
6 
6 
[1] 1


xlim_start   xlim_end 
         0  191154276 
[1] 0 1
xlim_start   xlim_end 
         0  191154276 
[1] 0 1
   start      end 
       0 59373566 
[1] 0 1
[1] "chrY"
[1] 4
6 
6 
[1] 1


Warning message:
In add_track(panel.fun = function(gr) { :
  `panel.fun` is deprecated, please use `panel_fun`.
> 
> for(chr in paste0("chr", 1:22)) {
+     print(get_cell_meta_data("xlim", category = chr, track = 1))
+     print(get_cell_meta_data("ylim", category = chr, track = 1))
+     print(get_cell_meta_data("extended_xlim", category = chr, track = 1))
+     print(get_cell_meta_data("extended_ylim", category = chr, track = 1))
+     print(get_cell_meta_data("original_xlim", category = chr, track = 1))
+     print(get_cell_meta_data("original_ylim", category = chr, track = 1))
+     print(get_cell_meta_data("name", category = chr, track = 1))
+     print(get_cell_meta_data("column", category = chr, track = 1))
+     print(get_cell_meta_data("row", category = chr, track = 1))
+     print(get_cell_meta_data("track", category = chr, track = 1))
+     cat("\n\n")
+ }
xlim_start   xlim_end 
         0  249250621 
[1] 0 1
xlim_start   xlim_end 
         0  249250621 
[1] 0 1
    start       end 
        0 249250621 
[1] 0 1
[1] "chr1"
[1] 1
1 
1 
[1] 1


xlim_start   xlim_end 
         0  243199373 
[1] 0 1
xlim_start   xlim_end 
         0  243199373 
[1] 0 1
    start       end 
        0 243199373 
[1] 0 1
[1] "chr2"
[1] 2
1 
1 
[1] 1


xlim_start   xlim_end 
         0  198022430 
[1] 0 1
xlim_start   xlim_end 
         0  198022430 
[1] 0 1
    start       end 
        0 198022430 
[1] 0 1
[1] "chr3"
[1] 3
1 
1 
[1] 1


xlim_start   xlim_end 
         0  191154276 
[1] 0 1
xlim_start   xlim_end 
         0  191154276 
[1] 0 1
    start       end 
        0 191154276 
[1] 0 1
[1] "chr4"
[1] 4
1 
1 
[1] 1


xlim_start   xlim_end 
         0  249250621 
[1] 0 1
xlim_start   xlim_end 
         0  249250621 
[1] 0 1
    start       end 
        0 180915260 
[1] 0 1
[1] "chr5"
[1] 1
2 
2 
[1] 1


xlim_start   xlim_end 
         0  243199373 
[1] 0 1
xlim_start   xlim_end 
         0  243199373 
[1] 0 1
    start       end 
        0 171115067 
[1] 0 1
[1] "chr6"
[1] 2
2 
2 
[1] 1


xlim_start   xlim_end 
         0  198022430 
[1] 0 1
xlim_start   xlim_end 
         0  198022430 
[1] 0 1
    start       end 
        0 159138663 
[1] 0 1
[1] "chr7"
[1] 3
2 
2 
[1] 1


xlim_start   xlim_end 
         0  191154276 
[1] 0 1
xlim_start   xlim_end 
         0  191154276 
[1] 0 1
    start       end 
        0 146364022 
[1] 0 1
[1] "chr8"
[1] 4
2 
2 
[1] 1


xlim_start   xlim_end 
         0  249250621 
[1] 0 1
xlim_start   xlim_end 
         0  249250621 
[1] 0 1
    start       end 
        0 141213431 
[1] 0 1
[1] "chr9"
[1] 1
3 
3 
[1] 1


xlim_start   xlim_end 
         0  243199373 
[1] 0 1
xlim_start   xlim_end 
         0  243199373 
[1] 0 1
    start       end 
        0 135534747 
[1] 0 1
[1] "chr10"
[1] 2
3 
3 
[1] 1


xlim_start   xlim_end 
         0  198022430 
[1] 0 1
xlim_start   xlim_end 
         0  198022430 
[1] 0 1
    start       end 
        0 135006516 
[1] 0 1
[1] "chr11"
[1] 3
3 
3 
[1] 1


xlim_start   xlim_end 
         0  191154276 
[1] 0 1
xlim_start   xlim_end 
         0  191154276 
[1] 0 1
    start       end 
        0 133851895 
[1] 0 1
[1] "chr12"
[1] 4
3 
3 
[1] 1


xlim_start   xlim_end 
         0  249250621 
[1] 0 1
xlim_start   xlim_end 
         0  249250621 
[1] 0 1
    start       end 
        0 115169878 
[1] 0 1
[1] "chr13"
[1] 1
4 
4 
[1] 1


xlim_start   xlim_end 
         0  243199373 
[1] 0 1
xlim_start   xlim_end 
         0  243199373 
[1] 0 1
    start       end 
        0 107349540 
[1] 0 1
[1] "chr14"
[1] 2
4 
4 
[1] 1


xlim_start   xlim_end 
         0  198022430 
[1] 0 1
xlim_start   xlim_end 
         0  198022430 
[1] 0 1
    start       end 
        0 102531392 
[1] 0 1
[1] "chr15"
[1] 3
4 
4 
[1] 1


xlim_start   xlim_end 
         0  191154276 
[1] 0 1
xlim_start   xlim_end 
         0  191154276 
[1] 0 1
   start      end 
       0 90354753 
[1] 0 1
[1] "chr16"
[1] 4
4 
4 
[1] 1


xlim_start   xlim_end 
         0  249250621 
[1] 0 1
xlim_start   xlim_end 
         0  249250621 
[1] 0 1
   start      end 
       0 81195210 
[1] 0 1
[1] "chr17"
[1] 1
5 
5 
[1] 1


xlim_start   xlim_end 
         0  243199373 
[1] 0 1
xlim_start   xlim_end 
         0  243199373 
[1] 0 1
   start      end 
       0 78077248 
[1] 0 1
[1] "chr18"
[1] 2
5 
5 
[1] 1


xlim_start   xlim_end 
         0  198022430 
[1] 0 1
xlim_start   xlim_end 
         0  198022430 
[1] 0 1
   start      end 
       0 59128983 
[1] 0 1
[1] "chr19"
[1] 3
5 
5 
[1] 1


xlim_start   xlim_end 
         0  191154276 
[1] 0 1
xlim_start   xlim_end 
         0  191154276 
[1] 0 1
   start      end 
       0 63025520 
[1] 0 1
[1] "chr20"
[1] 4
5 
5 
[1] 1


xlim_start   xlim_end 
         0  249250621 
[1] 0 1
xlim_start   xlim_end 
         0  249250621 
[1] 0 1
   start      end 
       0 48129895 
[1] 0 1
[1] "chr21"
[1] 1
6 
6 
[1] 1


xlim_start   xlim_end 
         0  243199373 
[1] 0 1
xlim_start   xlim_end 
         0  243199373 
[1] 0 1
   start      end 
       0 51304566 
[1] 0 1
[1] "chr22"
[1] 2
6 
6 
[1] 1


> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>