plotFeatures {tilingArray} | R Documentation |
Plot genomic features for a region along a chromosome
plotFeatures(gff, chr, xlim, strand, vpr, featureColorScheme=1, featureExclude=c("chromosome", "nucleotide_match", "insertion"), featureNoLabel=c("uORF", "CDS"), ...)
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). |
... |
additional arguments. |
This function is called by plotAlongChrom
when the gff
argument has been specified. It should not be called directly by the user.
Wolfgang Huber <huber@ebi.ac.uk>