plotAligned: Visualise reads aligned to genome intervals

In girafe: Genome Intervals and Read Alignments for Functional Exploration

Description

Visualise reads aligned to genome intervals

Usage

plotAligned(x, y, chr, start, end, plus.col = "#00441b",
   minus.col = "#283d78", gff, featureLegend = FALSE,
   gffChrColumn = "seq_name", gffTypeColumn="type",
   gffNameColumn="ID",
   featureExclude = c("chromosome", "nucleotide_match", "insertion"),
   showStrands="both", extraColors=NULL, ylim, highlight, main, ...)

Arguments

x	Object of class AlignedGenomeIntervals
y	This argument is only specified for compatibility with plot.default and not used in the function.
chr	string; on which chromosome is the region to plot
start	integer; start coordinate of the chromosome region to plot
end	integer; end coordinate of the chromosome region to plot
plus.col	which colour to use for the reads on the Plus strand
minus.col	which colour to use for the reads on the Plus strand
gff	Data frame containing annotation for genomic feature to be used to further annotate the plot. Note that it must include a column called “type” that indicates the type of each genomic feature (e.g. miRNA, gene etc.).
featureLegend	logical; should a legend that describes the colour code for the annotated genome features be appended at the bottom of the plot?
gffChrColumn	string; which column of the gff data.frame holds the chromosome identifier of each feature.
gffTypeColumn	string; which column of the gff data.frame holds the type/class identifier of each feature. Used for the colouring of features.
gffNameColumn	what is the column of the gff data.frame called that holds the identifier of the element that should be displayed in the plot; default: “name”
featureExclude	character; which kinds of annotated genome features specified in the gff are to be ignored for the plot
showStrands	string; which strands to show in the plot; defaults to “both”, but users can specify to show only the reads on “plus” or “minus” strand
extraColors	named character vector which allows the user to specify custom colours for feature types; colours must be specified in RGB format as hexadecimal strings starting with “#”, e.g. “#addfff” for light-blue
ylim	range of read numbers to plot (y-axis limits); if not specified they are computed from the data in the specified region
highlight	currently unused
main	string; main title to use for the plot
...	further arguments passed on to the more primitive plotting functions used

Details

This function implements the plot method for objects of class AlignedGenomeIntervals.

Value

Returns NULL; this function is called for the side-effect of creating the plot.

Note

This function was inspired by and borrows source code from the function plotAlongChrom in package tilingArray

Author(s)

Joern Toedling, Wolfgang Huber

See Also

AlignedGenomeIntervals-class

Examples

  A <- AlignedGenomeIntervals(
        start=c(1,8,10,20), end=c(5,15,16,25),
        chromosome=rep("chr1", each=4),
        strand=c("+","+","+","+"),
        sequence=c("ACATT","TATCGGAC","TCGGACT","GTAACG"),
        reads=c(5L, 2L, 4L, 7L) )
  M2 <- new("Genome_intervals_stranded",
            rbind(c(2,6), c(1,15), c(20,30)),
            closed = matrix(TRUE, ncol=2, nrow=3),
            annotation = data.frame(
              seq_name= factor(rep("chr1", 3)),
              inter_base= logical(3),
              strand=factor(rep("+", 3), levels=c("+","-")),
              alias=c("miRNA1","gene1","tRNA1"),
              type=c("miRNA","gene","tRNA")) )
  if (interactive())
    plot(A, M2, chr="chr1", start=0, end=35,
         nameColum="alias", showStrands="plus")

  if (interactive())
  ## use 'extraColors' to replace default colours (or to add new ones):
    plot(A, M2, chr="chr1", start=0, end=35, nameColum="alias",
         showStrands="plus", extraColors=c("tRNA"="#6666DD"))

  ## See also the examples in the vignette and on the manual page
  ##  of the class 'AlignedGenomeIntervals'

girafe documentation built on Nov. 8, 2020, 4:56 p.m.