OLIN (version 1.50.0)

sigxy.plot2: Visualisation of significance tests for spatial bias

Description

This function produces a 2D-plot visualizing the significance of spatial bias.

Usage

sigxy.plot2(object,Sp,Sn,color.lim=c(-3,3),...)

Arguments

object

object of class marrayRaw or marrayNorm

Sp

vector of false discovery rates or p-values for positive deviation of $median/mean of \code{M}$ as produced by fdrspatial or p.spatial

Sn

vector of false discovery rate or p-values for negative deviation of $median/mean of \code{M}$ as produced by fdrspatial or p.spatial

color.lim

limits of color range for plotting vector corresponding to log10(pS) and log10(nS)

...

Further optional graphical parameter for the image function generating the MXY plot

Details

The function sigxy.plot2 differs from sigxy.plot in its input arguments. The functionality is the same. For details, see sigxy.plot.

See Also

colorbar.sig, sigxy.plot, sigxy.plot,fdr.spatial2, p.spatial2, image

Examples

# To run these examples, "un-comment" them!
#
# LOADING DATA
# data(sw)
# CALCULATION OF SIGNIFICANCE OF SPOT NEIGHBOURHOODS
# For this illustration, N was chosen rather small. For "real" analysis, it should be larger.
# FDR <- fdr.spatial2(sw,delta=2,N=10,av="median",edgeNA=TRUE)
#
# SIGNIFICANCE PLOTS OF ARRAY 1
# sigxy.plot2(sw[,1],FDR$FDRp[[1]],FDR$FDRn[[1]],color.lim=c(-5,5),main="FDR")
# SIGNIFICANCE PLOTS OF ARRAY 3
# sigxy.plot2(sw[,3],FDR$FDRp[[3]],FDR$FDRn[[3]],color.lim=c(-5,5),main="FDR")
#