mxy.plot {OLIN} | R Documentation

## Generation of MXY plots

### Description

This function produce a MXY plot including a colour bar.

### Usage

    mxy.plot(V,Ngc,Ngr,Nsc,Nsr,color.lim=c(-1,1),xlab="Columns",ylab="Rows",...)

### Arguments

`V` | vector of real values typically logged ratios M. Alternatively, V can be an object of class marrayRaw or marrayNorm. In this case, the layout of the array does not need to be given.
`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

Spotted microarrays have generally a grid layout of form with `Ngc` columns and `Ngr` rows. Each block (or spot matrix) of the grid corresponds to a specific pin used for spotting. The blocks have generally `Nsc` columns and `Nsr` rows. The function `mxy.plot` generates a 2D-plot (MXY-plot) of the values of M across the array. M is given in form of the vector V. Note that this function assumes a specific mapping between the data points and the location of spot (i.e. the same mapping rule that is used for marrayRaw/marrayNorm objects (see the documentation of packet marray) The colour range of the MXY plot is centred around zero and follows the conventional colouring (green for negative, red for positive fold-changes). For a separate visualisation of the two channels, see function `fgbg.visu`.

### Author(s)

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

### See Also

`v2m`, `m2v`, `fgbg.visu`, `image`, `marrayRaw`

### Examples

    # LOADING DATA
    data(sw)

    # PLOTTING
    mxy.plot(maM(sw)[,1],Ngc=maNgc(sw),Ngr=maNgr(sw), Nsc=maNsc(sw),Nsr=maNsr(sw))

    # ALTERNATIVE
    mxy.plot(sw[,1])

[Package OLIN version 1.12.0 Index]