mxy2.plot {OLIN} | R Documentation

## Generation of MXY plots based on spot coordinates

### Description

This function produce a MXY plot with a colour bar. In contrast to `mxy.plot`, the plot is based on spot coordinates (instead on column and row index as proxies for spot location).

### Usage

    mxy2.plot(V,X,Y,Ngc,Ngr,Nsc,Nsr,color.lim=c(-1,1),xlab="X",ylab="Y",...)

### Arguments

`V` | vector of real values typically logged ratios M.
`X` | vector of x coordinates of spot locations
`Y` | vector of y coordinates of spot locations
`Ngc` | number of columns for the grid matrix
`Ngr` | number of rows for the grid matrix
`Nsc` | number of columns for the spot matrix
`Nsr` | number of rows for the spot matrix
`color.lim` | limits of color range for MXY plot
`xlab` | label of x-axis of MXY plot
`ylab` | label of y-axis of MXY plot
`...` | Further optional graphical parameter for the `image` function generating the MXY plot

### Details

The function `mxy2.plot` can be used to plot the distribution of `V` across the array. As `mxy.plot`, it mainly aims for the plotting of the distribution of logged fold changes. It differs from `mxy.plot` in the representation of spot location. The function `mxy.plot` uses the index of columns and rows as proxies for the spot location. The gaps between the grid matrices (spotted by different pins) are, therefore, not reproduced in the plot. A more accurate spatial plot is produced by `mxy2.plot`, which is based on the coordinates of the first column and first raw of the array. Assuming a regular rectangular print layout, gaps and the edges of the array are shown.

### Author(s)

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

### See Also

`mxy.plot`, `v2m`, `m2v`, `fgbg.visu`, `image`

### Examples

    # LOADING DATA
    data(sw)
    data(sw.xy)
    # PLOTTING
    mxy2.plot(maM(sw)[,1],X=sw.xy$X[,1],Y=sw.xy$Y[,1], Ngc=maNgc(sw),Ngr=maNgr(sw),
                       Nsc=maNsc(sw),Nsr=maNsr(sw))

[Package OLIN version 1.64.0 Index]