mxy2.plot: Generation of MXY plots based on spot coordinates

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

Description

This function produce a MXY plot with a colour bar. In contrast to mxy.plot, the plot is based on spot coordinates (instead on column and row index as proxies for spot location).

Usage

mxy2.plot(V,X,Y,Ngc,Ngr,Nsc,Nsr,color.lim=c(-1,1),xlab="X",ylab="Y",...) 

Arguments

V	vector of real values typically logged ratios M.
X	vector of x coordinates of spot locations
Y	vector of y coordinates of spot locations
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

The function mxy2.plot can be used to plot the distribution of V across the array. As mxy.plot, it mainly aims for the plotting of the distribution of logged fold changes. It differs from mxy.plot in the representation of spot location. The function mxy.plot uses the index of columns and rows as proxies for the spot location. The gaps between the grid matrices (spotted by different pins) are, therefore, not reproduced in the plot. A more accurate spatial plot is produced by mxy2.plot, which is based on the coordinates of the first column and first raw of the array. Assuming a regular rectangular print layout, gaps and the edges of the array are shown.

Author(s)

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

See Also

mxy.plot, v2m, m2v, fgbg.visu, image

Examples

# LOADING DATA
data(sw)
data(sw.xy)
# PLOTTING
mxy2.plot(maM(sw)[,1],X=sw.xy$X[,1],Y=sw.xy$Y[,1], Ngc=maNgc(sw),Ngr=maNgr(sw),
                   Nsc=maNsc(sw),Nsr=maNsr(sw))

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