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Last data update: 2014.03.03

R: A plotting function for chromosomes.

cPlot

R Documentation

A plotting function for chromosomes.

Description

Given a chromLocation object, will plot all the gene locations from that object.

Usage

cPlot(plotChroms, useChroms=chromNames(plotChroms),
      scale=c("relative","max"), fg="white", bg="lightgrey", 
      glen=0.4, xlab="", ylab="Chromosome",
      main = organism(plotChroms), ...)

Arguments

`plotChroms`	An object of type chromLocation which contains all the gene information to be plotted.
`useChroms`	A vector of chromosome names to be used in the plot. Default is to use all the chromosomes from the plotChroms object.
`scale`	Passed on to cScale as it's scale argument. Determines whether the graph is scaled on a relative or absolute basis.
`fg`	The colour to be used for the genes. Default is white.
`bg`	The colour to be used for the background of the plot. Defaults to lightgrey.
`glen`	A scaling factor applied to the plotted length of each gene. Defaults to 0.4 - it is recommended that this not be set larger then 0.5 as it will cause overlap between chromosomes.
`xlab`	A label for the x axis.
`ylab`	A label for the y axis.
`main`	A main label for the plot.
`...`	Additional graphics arguments, passed to `segments`, which is used to draw the vertical ticks.

Details

This function will first use the lengths of the chromosomes, stored in the object to create scaling factors for the X axis. Once the scaling factors are determined, the chromLocation object which is passed in is used to determine all the gene locations/strand information/etc, which is then plotted for the user.

Author(s)

Jeff Gentry

Examples

   ## A bit of a hack to not have a package dependency on hgu95av2
   ## but need to fiddle w/ the warn level to not fail the example anyways.

   curWarn <- options(warn=0)
   on.exit(options(curWarn), add=TRUE)
   if (require("hgu95av2.db")) {
       z <- buildChromLocation("hgu95av2")

       if (interactive()) {
           curPar <- par(ask=TRUE)
           on.exit(par(curPar), add=TRUE)
       }

       for (sc in c("max","relative"))
           cPlot(z,c("1","5","10","X","Y"),sc)
   } else print("This example can not be run without hgu95av2 data package")

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)

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Type 'demo()' for some demos, 'help()' for on-line help, or
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Type 'q()' to quit R.

> library(geneplotter)
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: lattice
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
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/geneplotter/cPlot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: cPlot
> ### Title: A plotting function for chromosomes.
> ### Aliases: cPlot
> ### Keywords: utilities
> 
> ### ** Examples
> 
>    ## A bit of a hack to not have a package dependency on hgu95av2
>    ## but need to fiddle w/ the warn level to not fail the example anyways.
> 
>    curWarn <- options(warn=0)
>    on.exit(options(curWarn), add=TRUE)
>    if (require("hgu95av2.db")) {
+        z <- buildChromLocation("hgu95av2")
+ 
+ #       if (interactive()) {
+            curPar <- par(ask=TRUE)
+            on.exit(par(curPar), add=TRUE)
+ #       }
+ 
+        for (sc in c("max","relative"))
+            cPlot(z,c("1","5","10","X","Y"),sc)
+    } else print("This example can not be run without hgu95av2 data package")
Loading required package: hgu95av2.db
Loading required package: org.Hs.eg.db


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