xmap.plot: Utility methods for quick graph generation

Description Usage Arguments Author(s) See Also Examples

View source: R/xmapbridge.R

Description

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

Usage

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  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

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  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. 1, 2018, 2:05 a.m.