Usage
plotFeatures(gff, chr, xlim, strand, vpr, featureColorScheme=1, featureExclude=c("chromosome", "nucleotide_match", "insertion"), featureNoLabel=c("uORF", "CDS"), ...)
Arguments
gff
data frame with genome annotation from the GFF file.
chr
integer of length 1 specifying the chromosome to plot the features for.
xlim
integer of length 2 with start and end coordinates (in bases) for plotting.
strand
character scalar which should be set to either + or - to
indicate which strand of DNA to plot the features from.
vpr
which viewport to plot the features in.
featureColorScheme
numeric scalar, used to select a color scheme for the
boxes representing genomic features such as coding sequences, ncRNAs etc.
Currently the only value supported is 1.
featureExclude
character vector of names of feature types (in
gff) that should not be plotted. Default is "chromosome", "nucleotide_match" and
"insertion". Additional possible candidates include: "ARS", "repeat\_region",
"repeat\_family" and "nc\_primary\_transcript".
featureNoLabel
character vector, names of feature types (in
gff) that should not be labelled with their names (if they are plotted).