Converts vector to matrix based on spot layout

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

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)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(OLIN)
Loading required package: locfit
locfit 1.5-9.1 	 2013-03-22
Loading required package: marray
Loading required package: limma
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/OLIN/v2m.Rd_%03d_medium.png", width=480, height=480)
> ### Name: v2m
> ### Title: Converts vector to matrix based on spot layout
> ### Aliases: v2m
> ### Keywords: manip
> 
> ### ** 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)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>