
getDasFeature
or adds them to an existing plot.
plotFeatures(df, col=NULL, col.start="start", col.end="end", col.id ="label", col.type="type", box.height=4, box.sep=2, pos.label=c("middle", "top", "bottom", "no"), new=TRUE, legend=TRUE, ...)
data.frame
with the features. Columns col.start,
col.end, col.id and col.type
must be present.
df
. If NULL
, automatic
rainbow coloring for different types will be used.
pos.label=="no"
,
labels are disabled.
new=FALSE
, boxes will be added
to an existing plot (so, coordinate system must be consistent).
plot.default
Notice that boxes will can be plotted overlaping the current open graphical device, so the x-coordinates must match.
getDasFeature
# This is UCSC Genome browser
setDasServer(server="http://genome.ucsc.edu/cgi-bin/das")
# Note that id now changes, we can retrieve it from getDasDsn()
source <- "sacCer3"
range <- GRanges(c("I"), IRanges(start=1, end=2500))
type <- c("sgdGene")
# We want the official genes from 'sdgGene' in the range I:1-2500
features <- getDasFeature(source, range, type)
print(features)
plotFeatures(features)
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