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
>
|
|