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

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)

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
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> 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/m2v.Rd_%03d_medium.png", width=480, height=480)
> ### Name: m2v
> ### Title: Converts matrix to vector based on spot layout
> ### Aliases: m2v
> ### Keywords: manip
> 
> ### ** 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)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>