scatterPlot {BeadExplorer}R Documentation

Pairwise scattergraph of data

Description

Plots a scattergraph of intensity data for two samples

Usage

scatterPlot(beadData, xcol, ycol, manifest=NULL, equalline=TRUE, equallinecol="red", equallinetype=1, identify=TRUE, lines=2, 
linescol="green", linestype=2, log=TRUE, xlab="", ylab="", highlight=TRUE, detection=0.99, 
highlightcol=c("red","blue","green"), legend=TRUE, ...)

Arguments

beadData Object of class beadData-class
xcol Numeric, column number to plot on x-axis
ycol Numeric, column number to plot on y-axis
manifest data.frame of manifest data - produced by readManifest
equalline Logcial, specifiying if an equality line should be plotted on the graph
equallinecol Colour to be used for the equality line
equallinetype Line type used for an equality line, see par -lty
identify Logcial, specifiying if an interactive point and click plot identification tool should be used
lines Numeric, a vector of fold change lines to plot
linescol Colour to be used for the fold change lines
linestype Line type to be used for the fold change lines , see par-lty
log Logcial, specifying if log2 axes should be used
xlab A label for the x-axis
ylab A label for the y-axis
highlight Logcial, specifying whether to highlight the points by detection score
detection The illumina cut-off detection score called as 'Present'
highlightcol A vector of colours to be used for present calls
legend Logical, specifying if a legend should be drawn
... Arguments passed to plot

Details

This function produces a scattergraph of two samples. Use identify to allow the clicking of data points with a left-click of the mouse. Finish selecting data points by right-clicking the mouse and 'stop'. Data (eg log2 intensity, ratio, detection scores) of the selected points is outputted to the console. Using the manifest argument will also output gene annotation information of selected points.

Value

If identify is used, information regarding the points selected by the mouse is returned

Author(s)

Gareth Elvidge gareth.elvidge@well.ox.ac.uk

See Also

pairs

Examples


data(examplebeadData)
scatterPlot(examplebeadData, 1,2)

#to include annotation data:-
#man<-readManifest("d:\Bead_Set_Manifest\Human_WG-6.csv")
#scatterPlot(examplebeadData, 1, 2, man)

[Package BeadExplorer version 1.2.0 Index]