v2m: Converts vector to matrix based on spot layout

In OLIN: Optimized local intensity-dependent normalisation of two-color microarrays

Description

This functions converts a vector to a matrix based on a given spot layout. Optionally, it produces a 2D-plot.

Usage

v2m(V,Ngc,Ngr,Nsc,Nsr,visu=FALSE,color.lim=c(-1,1),xlab="Columns",ylab="Rows",...) 

Arguments

V	vector 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 FALSE, MXY plot is generated.
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 parameters for the image function generating the MXY plot

Details

The function v2m converts a vector V (as e.g. derived by maM(object)[,index]) to a matrix representing the spatial distribution of the values of V across the array. 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.) The validity of this mapping should be carefully checked (see also the documentation of packet marray.) 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 v2n does not include a colour bar. To have a colour included, you can use mxy.plot.

Value

A 2D-matrix with (Ngc*Nsc) columns and (Ngr*Nsr) is produced. This matrix represents the spatial distribution of the values of vector V given the print-layout.

Author(s)

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

See Also

mxy.plot, m2v, marrayRaw

Examples

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

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

OLIN documentation built on Nov. 8, 2020, 7:44 p.m.