plotAlongChrom {tilingArray}R Documentation

Plot the results of segmentation along a chromosomal region

Description

Plot the results of segmentation along a chromosomal region

Usage

plotAlongChrom(chr, coord, highlight, segObj, y, ylim, nrBasesPerSeg, 
                      probeAnno, gff,
                      colors, featColScheme=1,
                      isDirectHybe=FALSE, scoreShow = "pt", 
                      haveNames=TRUE, haveLegend=TRUE, main="", 
                      pointSize=unit(0.6, "mm"))

Arguments

chr integer of length 1 with the number of the chromosome for which to make the plot.
coord integer of length 2 with start and end coordinates of the plot.
highlight optional, list with two elements: a single numeric value coord and a character strand. If present, this position is marked by a vertical red bar on the coordinate axis.
segObj environment containing three types of data
  • microarray intensities in along-chromosome order,
  • a segmentation (output of findSegments),
  • a data.frame named segScore with segment scores; can be missing iff nrBasesPerSeg is present,
  • a numeric scalar names theThreshold, which is used to draw a horizontal "threshold" line in the plot.
See also Paragraph Intensities in the Details section. This is currently simply an environment that is expected to contain certain objects with certain names. In future version, this is may be replaced by a proper S4 object.
y numeric vector of intensities from an array, see Paragraph Intensities in the Details section.
ylim numeric vector of length two with y-axis limits.
nrBasesPerSeg numeric scalar. If segObj does not contain a segScore data.frame, then this parameter allows to choose the parameter which controls the number of segments in the segmentation (called S in the paper). In particular, this parameter specifies the average length of segments, measured in bases, thus one value can be used for all chromosomes.
probeAnno environment with probe annotations, see vignette.
gff data frame with genome annotation from the GFF file.
colors named character vector, optional. If missing, the following default is used: c("+"="#00441b", "-"="#081d58", "duplicated"="grey", "cp"="#101010", "highlight"="red", "threshold"="grey"), where the first three elements refer to colors of data points and the last three to those of lines in the plot.
featColScheme numeric scalar, used to select a color scheme for the boxes representing genomic features such as coding sequences, ncRNAs etc. Currently the values 1 and 2 are supported.
isDirectHybe logical scalar: if TRUE, the mapping of probes to genomic strands is reversed with respect to the default. This is appropriate for data from a direct RNA hybridization that used no reverse transcription.
scoreShow character: name of a column in segScore that is to be used for the coloring of the segments.
haveNames logical; should their names be added to the feature symbols?
haveLegend logical: should the plot contain a legend?
main character: plot title.
pointSize unit object: point size used for the probe intensities scatterplot.

Details

Intensities: There are two alternative, mutually exclusive ways of providing the intensities to be plotted to this function.

  1. Via the parameters y and probeAnno. Then, y is a vector of intensities, and probeAnno is an environment that contains integer vectors with start positions along the chromosomes and indices in y of the probes. For example, the start positions and indices of probes for the + strand of chromosome 1 would be described by environment elements "1.+.start" and "1.+.index", respectively.
  2. Via the parameter segRes. In that case, the intended workflow for using this function is as follows: First, use the script segment.R to generate a segmentation. This can be run in parallel on several processors, separately for each chromosome and strand. The results of this are stored in files of the name 1.+.rda, 1.-.rda, 2.+.rda, and so forth, typically within a dedicated directory. Then, the script viewsegmentation.R can be used to view the segmentation results. It collects the R objects in these .rda files into the environment segRes, with which it calls this function.

    Furthermore, the script scoreSegments.R can be used to calculate scores for each segment, which can be passed to this function using the segRes argument.

Author(s)

Wolfgang Huber <huber@ebi.ac.uk>

Examples

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[Package tilingArray version 1.2.0 Index]