A function for mapping chromosome length to a number of points.

Description

Given a number of points (generally representing the number of points on a plot's axis), and a vector of chromosome lengths - will generate a vector of the same length as the one passed in containing scaling factors for each chromosome.

Usage

cScale(points, cLengths, method=c("max", "relative"), chrom)

Arguments

Details

The scale factor is calculated in a manner based on the method argument. If method is max, the factor is derived by dividing the points argument by each chromosome's length (in base pairs). If the method chosen is relative, then the scale is determined by dividing the points argument by the maximum chromsome length, and applying that value to each chromosome.

Author(s)

Jeff Gentry

See Also

cPlot

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(warn), add=TRUE)
   if (require("hgu95av2.db")) {
      z <- buildChromLocation("hgu95av2")

     for (sc in c("max","relative"))
       scale <- cScale(1000, chromLengths(z),sc,"Y")
   } else print("This example needs the hgu95av2 data package")

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> 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/cScale.Rd_%03d_medium.png", width=480, height=480)
> ### Name: cScale
> ### Title: A function for mapping chromosome length to a number of points.
> ### Aliases: cScale
> ### 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(warn), add=TRUE)
>    if (require("hgu95av2.db")) {
+       z <- buildChromLocation("hgu95av2")
+ 
+      for (sc in c("max","relative"))
+        scale <- cScale(1000, chromLengths(z),sc,"Y")
+    } else print("This example needs the hgu95av2 data package")
Loading required package: hgu95av2.db
Loading required package: org.Hs.eg.db


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> dev.off()
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