m2v {OLIN} | R Documentation |
This function converts a matrix based on the spatial layout of spots to a vector. Optionally, a 2D-plot is produced.
m2v(M,Ngc,Ngr,Nsc,Nsr,visu=FALSE,color.lim=c(-1,1),xlab="Columns",ylab="Rows",...)
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 |
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.
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.
Matthias E. Futschik (http://itb.biologie.hu-berlin.de/~futschik)
# 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)