sigxy.plot: Visualisation of significance tests for spatial bias
In OLIN: Optimized local intensity-dependent normalisation of two-color microarrays

Description Usage Arguments Details Author(s) See Also Examples

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

1	sigxy.plot(Sp,Sn,color.lim=c(-3,3),...)

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

The function sigxy.plot produces a 2d-plot presenting the significance (pS,nS) generated by fdrint or p.spatial. The significance Sp for positive median/mean of \code{M} of spatial spot neighbourhoods are presented by red colour; the significance(Sn) for negative median/mean of \code{M} of spatial spot neighbourhoods are presented by green colour.

Matthias E. Futschik (http://itb.biologie.hu-berlin.de/~futschik)

colorbar.sig, fdr.spatial, p.spatial, image, p.spatial

# To run these examples, "un-comment" them!
#
# LOADING DATA
# data(sw)
#
# M <- v2m(maM(sw)[,1],Ngc=maNgc(sw),Ngr=maNgr(sw),
#                Nsc=maNsc(sw),Nsr=maNsr(sw),main="MXY plot of SW-array 1")
#
# CALCULATION OF SIGNIFICANCE OF SPOT NEIGHBOURHOODS
# This can take a while! For testing, you may choose a smaller N.
# FDR <- fdr.spatial(M,delta=2,N=100,av="median",edgeNA=TRUE)
# sigxy.plot(FDR$FDRp,FDR$FDRn,color.lim=c(-5,5),main="FDR")
# 
# LOADING NORMALISED DATA
# data(sw.olin)
# M <- v2m(maM(sw.olin)[,1],Ngc=maNgc(sw.olin),Ngr=maNgr(sw.olin),
#                Nsc=maNsc(sw.olin),Nsr=maNsr(sw.olin),main="MXY plot of SW-array 1")
#
# CALCULATION OF SIGNIFICANCE OF SPOT NEIGHBOURHOODS
# FDR <- fdr.spatial(M,delta=2,N=100,av="median",edgeNA=TRUE)
# VISUALISATION OF RESULTS
# sigxy.plot(FDR$FDRp,FDR$FDRn,color.lim=c(-5,5),main="FDR")
#
#
# CALCULATION OF SIGNIFICANCE OF SPOT NEIGHBOURHOODS 
# P <- p.spatial(M,delta=2,N=-1,av="median",p.adjust.method="holm")
# VISUALISATION OF RESULTS
# sigxy.plot(P$Pp,P$Pn,color.lim=c(-5,5),main="FDR")