mxy.plot: Generation of MXY plots

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

Description

This function produce a MXY plot including a colour bar.

Usage

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

Arguments

V	vector of real values typically logged ratios M. Alternatively, V can be an object of class marrayRaw or marrayNorm. In this case, the layout of the array does not need to be given.
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
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 graphical parameter for the image function generating the MXY plot

Details

Spotted microarrays have generally a grid layout of form with Ngc columns and Ngr rows. Each block (or spot matrix) of the grid corresponds to a specific pin used for spotting. The blocks have generally Nsc columns and Nsr rows. The function mxy.plot generates a 2D-plot (MXY-plot) of the values of M across the array. M is given in form of the vector V. 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 (see the documentation of packet marray) The colour range of the MXY plot is centred around zero and follows the conventional colouring (green for negative, red for positive fold-changes). For a separate visualisation\ of the two channels, see function fgbg.visu.

Author(s)

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

See Also

v2m, m2v, fgbg.visu, image, marrayRaw

Examples

# LOADING DATA
data(sw)

# PLOTTING
mxy.plot(maM(sw)[,1],Ngc=maNgc(sw),Ngr=maNgr(sw), Nsc=maNsc(sw),Nsr=maNsr(sw))

# ALTERNATIVE
mxy.plot(sw[,1])

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