xmap.plot {xmapbridge} | R Documentation

## Utility methods for quick graph generation

### 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 )

[Package xmapbridge version 1.48.0 Index]