m2v {OLIN} | R Documentation

## Converts matrix to vector based on spot layout

### Description

This function converts a matrix based on the spatial layout of spots to a vector. Optionally, a 2D-plot is produced.

### Usage

    m2v(M,Ngc,Ngr,Nsc,Nsr,visu=FALSE,color.lim=c(-1,1),xlab="Columns",ylab="Rows",...)

### Arguments

`M` | Matrix of real values
`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
`visu` | If TRUE, MXY plot is generated.
`color.lim` | limits of colour range for 2D-plot
`xlab` | label of x -axis of 2D-plot
`ylab` | label of y-axis of 2D-plot
`...` | Further optional parameters for the `image` function generating the MXY plot

### Details

The function `m2v` rearranges the values of a matrix `M` corresponding to the intensity values on the array to a vector `V`. The matrix `M` may have been generated by e.g. `v2m`. The order of values in `V` follows the convention of marrayRaw objects. In fact, the transformation of `m2v` is the reverse of `v2m` (assuming the arguments are kept the same.) Note that these functions assume 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.) The validity of the mappings should be carefully checked (see also the documentation of the marray package.) The option for spatial visualisation is rather restricted to logged fold-changes as the corresponding colour range is centred around zero and follows the conventional colouring (green for negative, red for positive fold-changes). The MXY plot produced by `m2v` does not include a colour-bar. To have a colour included, `mxy.plot` can be used.

### Value

A vector `V` of length `((Ngc*Nsc)*(Ngr*Nsr))` is produced. The values of `V` represents the spatial distribution of the values of vector `V` given the print-layout. Optionally, a 2D-plot of `M` is generated.

### Author(s)

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

### See Also

`v2m`, `mxy.plot`

### Examples

    # LOADING DATA NOT-NORMALISED
    data(sw)
    # CONVERSION FROM VECTOR TO MATRIX
    M <- v2m(maM(sw)[,1],Ngc=maNgc(sw),Ngr=maNgr(sw),Nsc=maNsc(sw),Nsr=maNsr(sw),visu=TRUE)

    # BACK-CONVERSION FROM MATRIX TO VECTOR
    V <- m2v(M,Ngc=maNgc(sw),Ngr=maNgr(sw),Nsc=maNsc(sw),Nsr=maNsr(sw),visu=TRUE)

[Package OLIN version 1.70.0 Index]