mxy.abs.plot: Generation of MXY plots of absolute values

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

Description

This function produce a MXY plot of absolute values of M including a colour bar.

Usage

mxy.abs.plot(V,Ngc,Ngr,Nsc,Nsr,color.lim,color="red",xlab="Columns",ylab="Rows",...) 

Arguments

V	vector of positive 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
color.lim	limits of color range for MXY plot
color	color to be used for plot: “red” (default) or “green”
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 mxy.abs.plot is similar to function mxy.plot. Details can therefore be found at mxy.plot. Two differences, however, exist: First, mxy.abs.plot plots the absolute value of V and second, “red” (default) or “green” can be chosen as colour of plotting. Hence, mxy.abs.plot facilitates the inspection of spatial artifacts in single fluorescence channels.

Author(s)

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

See Also

v2m, m2v, colorbar.mxy.abs, fgbg.visu, image

Examples

# LOADING DATA
data(sw)
# PLOTTING OF ABSOLUTE LOGGED FOLD-CHANGES
mxy.plot(abs(maM(sw)[,1]),Ngc=maNgc(sw),Ngr=maNgr(sw),Nsc=maNsc(sw),Nsr=maNsr(sw))

# PLOTTING SPATIAL DISTRIBUTION OF SINGLE-CHANNEL INTENSITIES
mxy.abs.plot(maRf(sw)[,1],color.lim=c(0,10000),Ngc=maNgc(sw),Ngr=maNgr(sw),
             Nsc=maNsc(sw),Nsr=maNsr(sw))
mxy.abs.plot(maGf(sw)[,1],color.lim=c(0,10000),color="green",Ngc=maNgc(sw),Ngr=maNgr(sw),
             Nsc=maNsc(sw),Nsr=maNsr(sw))

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