A function for marking specific probes on a cPlot.

Description

Given a set of probes, will highlight them in the color desired on a plot which has already been created via the function cPlot().

Usage

cColor(probes, color, plotChroms, scale=c("relative","max"), glen=0.4,
       ...)

Arguments

Details

It is important to call the function cPlot() first. This function will then search for the specific locations of the probes desired, which are contained within the plotChroms instance of a chromLocation class. It will then pass these on to the plotting routine to highlight the desired locations. NOTE: It is important that plotChroms, scale and glen parameters are the same as used for cPlot().

Author(s)

Jeff Gentry

See Also

cPlot, chromLocation-class

Examples

  if (require("hgu95av2.db")) {
    z <- buildChromLocation("hgu95av2")
    cPlot(z)
    probes <- c("266_s_at", "31411_at", "610_at", "failExample")
    cColor(probes, "red", z)
    probes2 <- c("960_g_at", "41807_at", "931_at", "39032_at")
    cColor(probes2, "blue", z)
  } else
    print("Need hgu95av2.db data package for the example")
  

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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> 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/cColor.Rd_%03d_medium.png", width=480, height=480)
> ### Name: cColor
> ### Title: A function for marking specific probes on a cPlot.
> ### Aliases: cColor
> ### Keywords: utilities
> 
> ### ** Examples
> 
>   if (require("hgu95av2.db")) {
+     z <- buildChromLocation("hgu95av2")
+     cPlot(z)
+     probes <- c("266_s_at", "31411_at", "610_at", "failExample")
+     cColor(probes, "red", z)
+     probes2 <- c("960_g_at", "41807_at", "931_at", "39032_at")
+     cColor(probes2, "blue", z)
+   } else
+     print("Need hgu95av2.db data package for the example")
Loading required package: hgu95av2.db
Loading required package: org.Hs.eg.db


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> dev.off()
null device 
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