cPlot: A plotting function for chromosomes.

In geneplotter: Graphics related functions for Bioconductor

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

See Also

cScale, cColor, chromLocation-class

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")

Example output

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, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, 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, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

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 object is masked from 'package:base':

    expand.grid

Loading required package: XML
Loading required package: hgu95av2.db
Loading required package: org.Hs.eg.db

geneplotter documentation built on Nov. 8, 2020, 7:13 p.m.