sigxy.plot {OLIN} | R Documentation

## 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.

### 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 1.72.0 Index]