xmap.plot {xmapbridge} | R Documentation |
These methods attempt to provide a simpler interface for generating X:Map graphs.
xmap.plot( x, y, species=c("homo_sapiens","mus_musculus","rattus_norvegicus"), chr, xlim, ylim, main, sub, type=c("scatter", "line", "bar", "step", "area", "steparea"), xlab, ylab = "value", col, dp=2, projectid ) xmap.points( x, y, type=c("scatter", "line", "bar", "step", "area", "steparea"), xlab, col, dp=2, graphid )
x |
The points for the x-axis of this plot. These points must be offsets from the start of the graph, and not their actual chromosomal location |
y |
The points for the y-axis of this plot. Points where min>y or y >max will not be displayed |
species |
The species that this graph is to be drawn on |
chr |
A string representing the chromosome this graph is to be drawn on |
xlim |
A range object describing the min and max BP for this graph. If ommitted, we call range on the x parameter |
ylim |
The maximum and minimum Y value for the graph. If ommitted, we call range on the y parameter |
main |
The main title |
sub |
A sub-title for this graph |
type |
The type of graph you wish to draw |
xlab |
The label for this plot |
ylab |
The label for the yaxis of this graph |
col |
The colour of the graph defined as an integer in the format 0xAARRGGBB. See xmap.col |
dp |
The number of decimal places you want to save for the y-coordinates |
projectid |
The projectid (returned by xmap.project.new and as a list from xmap.project.list . If this is not passed, on the first time of calling a new project will be created, and will be used on all subsequent calls) |
graphid |
The graphid returned by xmap.graph.new or xmap.graph.list . If this is not passed, it will use the last graph generated by xmap.plot . |
Tim Yates
xmap.col
xmap.project.new
xmap.project.list
xmap.project.load
xmap.project.save
xmap.project.delete
xmap.graph.new
xmap.graph.list
xmap.graph.load
xmap.graph.save
xmap.graph.delete
xmap.plot.new
xmap.plot.list
xmap.plot.load
xmap.plot.save
xmap.plot.delete
x <- seq( 1000, 100000, by = 1000 ) y <- runif( length( x ), -10, 10 ) # This will create a new project, and graph, and add a plot to it xmap.plot( x, y, species="homo_sapiens", "1", main="A quick graph", sub="Sub heading", type="area", xlab="Plot 1", col=0xAAFFBB00 ) # This will add another plot to the same graph xmap.points( x, y, type="area", xlab="Plot 2", col=0xAA0000FF )