xmap.plot: Utility methods for quick graph generation

In xmapbridge: Export plotting files to the xmapBridge for visualisation in X:Map

Description

These methods attempt to provide a simpler interface for generating X:Map graphs.

Usage

  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 )

Arguments

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.

Author(s)

Tim Yates

See Also

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

Examples

  
  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 )
  

xmapbridge documentation built on Nov. 8, 2020, 6:46 p.m.