sigxy.plot {OLIN}R Documentation

Visualisation of significance tests for spatial bias

Description

This function produce 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 M as produced by fdrspatial or p.spatial
Sn matrix of false discovery rate or p-values for negative deviation of median/mean of 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 M of spatial spot neighbourhoods are presented by red colour; the significance(Sn) for negative median/mean of M of spatial spot neighbourhoods are presented by green colour.

Author(s)

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

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")


[Package OLIN version 1.3.2 Index]