Generation of MXY plots based on spot coordinates

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

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))

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(OLIN)
Loading required package: locfit
locfit 1.5-9.1 	 2013-03-22
Loading required package: marray
Loading required package: limma
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/OLIN/mxy2.plot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: mxy2.plot
> ### Title: Generation of MXY plots based on spot coordinates
> ### Aliases: mxy2.plot
> ### Keywords: hplot
> 
> ### ** 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))
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>