sigxy.plot2 {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.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 `M` as produced by `fdrspatial` or `p.spatial`
`Sn` | vector 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.plot2` differs from `sigxy.plot` in its input arguments. The functionality is the same. For details, see `sigxy.plot`.

### Note

This function will be merged with `sigxy.plot` in future versions.

### Author(s)

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

### See Also

`colorbar.sig`, `sigxy.plot`, `\code{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")
    #

[Package OLIN version 1.6.0 Index]