xmapbridge (version 1.30.0)

xmap.files: Underlying xmap methods for manipulating projects, graphs, and plots

Description

These methods are used to control xmap.projects, xmap.graphs and xmap.plots

A project contains one or more graphs, and a graph can contain one or more plots (each plot can have a different style)

A simpler method to generate X:Map graphs is to use the xmap.plot and xmap.points methods.

The xmap.debug method was introduced as otherwise the vignette would not print out id values as it was supposed to. For some reason Sweave ignores the show and as.character methods being overridden, and simply does its own thing.

Usage

xmap.debug( idobject, newlines=FALSE )
  xmap.project.new( name ) xmap.project.list() xmap.project.load( projectid ) xmap.project.save( projectid, data ) xmap.project.delete( projectid )
  xmap.graph.new( projectid, name, desc, min, max, chr, start, stop, ylab="value", species=c("homo_sapiens", "mus_musculus", "rattus_norvegicus") ) xmap.graph.list( projectid ) xmap.graph.load( graphid ) xmap.graph.save( graphid, data ) xmap.graph.delete( graphid )
  xmap.plot.new( graphid, name, x, y,  type=c("scatter", "line", "bar", "step", "area", "steparea"), col = NULL, dp = 2 ) xmap.plot.list( graphid ) xmap.plot.load( plotid ) xmap.plot.save( plotid, data, x, y, dp = 2 ) xmap.plot.delete( plotid )

Arguments

idobject

An id object for an xmapbridge project, graph or plot

newlines

Should the resultant string be nicely formatyted with newline characters?

name

The name for this object (stored in the NAME variable of the list returned by load)

projectid

The projectid (returned by xmap.project.new and as a list from xmap.project.list)

data

This is a list object for this particular object type

desc

The description for this item

min

The minimum y value for the graph

max

The maximum y value for the graph

chr

A string representing the chromosome this graph is to be drawn on

start

The BP that this graph should start on

stop

The BP that this graph reaches until. Must be greater than start

ylab

The label for the yaxis of this graph

species

The species that this graph is to be drawn on

graphid

The graphid returned by xmap.graph.new or xmap.graph.list

type

The type of graph you wish to draw

col

The colour of the graph defined as an integer in the format 0xAARRGGBB. See xmap.col

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

dp

The number of decimal places you want to save for the y-coordinates

plotid

The plotid which is returned by xmap.plot.new or xmap.plot.list

Value

xmap.graph.new returns the graphid of the created graph xmap.graph.list returns a vector of all graphs contained within the given project xmap.graph.load returns a list containing the parameters for the given graph xmap.graph.save

See Also

xmap.plot xmap.points xmap.col http://xmap.picr.man.ac.uk

Examples

  
  # Create a new project
  projectid <- xmap.project.new( "A quick project" )

  # Create a graph in this project covering 100K bases on chromosome 1
  graphid <- xmap.graph.new( projectid, "A quick graph", "This is a quick graph", 
                            -10, 10, "1", 5000, 105000, species="homo_sapiens" )

  # Make our datasets
  x <- seq( 1000, 100000, by = 1000 )
  y <- runif( length( x ), -10, 10 )

  # Then add a plot to this graph
  xmap.plot.new( graphid, "Graph 1", x, y, type="area", col=0xAAFFEE00 )

  # And another one, in a different colour  
  a <- xmap.plot.new( graphid, "Graph 2", x, y, type="scatter", col=0xAA0000FF )
  
  cat( xmap.debug( a, newlines=TRUE ) )

  # At this point, we should be able to see the graphs using the XMapBridge application

  # Clean up our project file...
  xmap.project.delete( projectid )