R Graphical Manual

Browse All

Last data update: 2014.03.03

R: Generation of MXY plots

mxy.plot

R Documentation

Generation of MXY plots

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)

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])

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/mxy.plot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: mxy.plot
> ### Title: Generation of MXY plots
> ### Aliases: mxy.plot
> ### Keywords: hplot
> 
> ### ** 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])
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>