comparisonPlot: Plot a vertical layout of panels for the comparison of...

In tilingArray: Transcript mapping with high-density oligonucleotide tiling arrays

Description

This function is used for Figure 5 in the David et al. (PNAS 2006) paper and in the Huber et al. methods paper.

Usage

comparisonPlot(x, y, xscale=range(x), yscale, anno, ticks, pch=20, cex=1, bgcol="#f2f2f2")

Arguments

x	numeric vector.
y	list of numeric vector, each of same length as x.
xscale	numeric vector of length 2.
yscale	matrix with 2 rows and columns corresponding to the elements of x.
anno	dataframe with columns start, end, and name, each row corresponds to one gene CDS to be plotted at the bottom.
ticks	numeric vector, where to plot the ticks.
pch	A numeric or character vector indicating what sort of plotting symbol to use, see grid.points.
cex	Multiplier applied to fontsize, see gpar.
bgcol	Color to use as background for some of the plot panels.

Value

Function is called for its side-effect.

Author(s)

W. Huber [e-mail]

References

...

Examples

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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, basename, cbind, colMeans, colSums, colnames,
    dirname, 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: pixmap
Warning message:
In read.dcf(con) :
  URL 'http://bioconductor.org/BiocInstaller.dcf': status was 'Couldn't resolve host name'

tilingArray documentation built on Nov. 8, 2020, 10:59 p.m.