OLIN (version 1.50.0)

sigxy.plot: Visualisation of significance tests for spatial bias

Description

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

Usage

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

Arguments

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

Details

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.

See Also

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

Examples

# 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")