Paramater class for plotting idiograms

Description

Paramater class for plotting idiograms

Usage

## S4 method for signature 'IdiogramParams'
show(object)

Arguments

Slots

seqnames

length-one character vector providing chromosome name

seqlengths

length-one numeric vector indicating size of chromosome

unit

character string indicating unit for genomic position (default is 'kb')

genome

character string indicating genome build

box

a list of parameters for plotting the box around the part of the idiogram that is plotted.

Examples

if(require(BSgenome.Hsapiens.UCSC.hg18) && require(grid)){
   si <- seqinfo(BSgenome.Hsapiens.UCSC.hg18)
   iparam <- IdiogramParams(seqnames="chr1",
                            genome="hg18",
                            seqlengths=seqlengths(si)["chr1"],
                            box=list(xlim=c(20e6L, 25e6L), color="blue", lwd=2))
   iparam
   idiogram <- plot(iparam)
   vp <- viewport(x=0.05, y=0.8, width=unit(0.9, "npc"), height=unit(0.2, "npc"),
                  name="vp1", just=c("left", "bottom"))
   grid.newpage()
   pushViewport(vp)
   print(idiogram, vp=vp, newpage=FALSE)
}

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(VanillaICE)
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: GenomicRanges
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: IRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Welcome to VanillaICE version 1.34.0
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/VanillaICE/IdiogramParams-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: IdiogramParams-class
> ### Title: Paramater class for plotting idiograms
> ### Aliases: IdiogramParams-class show,IdiogramParams-method
> 
> ### ** Examples
> 
> if(require(BSgenome.Hsapiens.UCSC.hg18) && require(grid)){
+    si <- seqinfo(BSgenome.Hsapiens.UCSC.hg18)
+    iparam <- IdiogramParams(seqnames="chr1",
+                             genome="hg18",
+                             seqlengths=seqlengths(si)["chr1"],
+                             box=list(xlim=c(20e6L, 25e6L), color="blue", lwd=2))
+    iparam
+    idiogram <- plot(iparam)
+    vp <- viewport(x=0.05, y=0.8, width=unit(0.9, "npc"), height=unit(0.2, "npc"),
+                   name="vp1", just=c("left", "bottom"))
+    grid.newpage()
+    pushViewport(vp)
+    print(idiogram, vp=vp, newpage=FALSE)
+ }
Loading required package: BSgenome.Hsapiens.UCSC.hg18
Loading required package: BSgenome
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:VanillaICE':

    deletion

Loading required package: rtracklayer
Loading required package: grid
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>