idiograb

Description

idiograb reads the position of the graphics pointer when the (first) mouse button is pressed. idiogram also reads a second position of the graphics pointer after another mouse button press. The two points selected are used to define a diagonal line from which a bounding box will be constructed. It then retrieves the gene identifiers of the points that lie within the bounding box.

Usage

idiograb(idio, show.box = TRUE, brush = NULL, ...)

Arguments

Details

Coordinates can be passed in a plotting structure (a list with x, y, and labels components). Typically this is generated from a call to idiogram.

The points selected are used to define the top-left and bottom-right locations or the bottom-left and top-right locations for bounding box. These locations can be selected in any order. A character vector of the labels of all the points that lie within the selected region is returned.

Value

A character vector of gene identifiers

Author(s)

Karl Dykema <karl.dykema@vai.org>

See Also

idiogram

Examples

data(idiogramExample)
ip <- idiogram(colo.eset[,1],ucsf.chr,chr="1")
if(interactive()) idiograb(ip,brush="red")

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(idiogram)
Loading required package: Biobase
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

Welcome to Bioconductor

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

Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: XML
Loading required package: plotrix
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/idiogram/idiograb.Rd_%03d_medium.png", width=480, height=480)
> ### Name: idiograb
> ### Title: idiograb
> ### Aliases: idiograb
> ### Keywords: iplot
> 
> ### ** Examples
> 
> data(idiogramExample)
> ip <- idiogram(colo.eset[,1],ucsf.chr,chr="1")
> #if(interactive()) idiograb(ip,brush="red")
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>