m2v: Converts matrix to vector based on spot layout

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

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)

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