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Last data update: 2014.03.03

R: Plot 1D graph of results from between group analysis

between.graph

R Documentation

Plot 1D graph of results from between group analysis

Description

Plots a 1D graph, of results of between group analysis similar to that in Culhane et al., 2002.

Usage

between.graph(x, ax = 1, cols = NULL, hor = TRUE, scaled=TRUE, centnames=NULL, varnames=NULL, ...)

Arguments

`x`	Object of the class `bga` resulting from a `bga` analysis.
`ax`	Numeric. The column number of principal component ($ls and $li) to be used. Default is 1. This is the first component of the analysis.
`cols`	Vector of colours. By default colours are obtained using `getcol`
`hor`	Logical, indicating whether the graph should be plotted horizontally or vertically. The default is a horizontal plot.
`scaled`	Logical, indicating whether the coordinates in the graph should be scaled to fit optimally in plot. Default is TRUE
`centnames`	A vector of variables labels. Default is NULL, if NULL the row names of the centroid $li coordinates will be used.
`varnames`	A vector of variables labels. Default is NULL, if NULL the row names of the variable $ls coordinates will be used.
`...`	further arguments passed to or from other methods

Details

This will produce a figure similar to Figure 1 in the paper by Culhane et al., 2002.

between.graph requires both samples and centroid co-ordinates ($ls, $li) which are passed to it via an object of class bga. If cases are to be coloured by class, it also requires a $fac factor which is also passed to it via an object of class bga.

To plot a 1D graph from other multivariate analysis such as PCA (dudi.pca), COA (dudi.coa), or coinertia analysis. Please use graph1D.

Author(s)

Aedin Culhane

References

Culhane AC, et al., 2002 Between-group analysis of microarray data. Bioinformatics. 18(12):1600-8.

Examples

data(khan)
if (require(ade4, quiet = TRUE)) {
khan.bga<-bga(khan$train, khan$train.classes)
}

between.graph(khan.bga)
between.graph(khan.bga, ax=2, lwd=3, cex=0.5, col=c("green","blue", "red", "yellow"))
between.graph(khan.bga, ax=2,  hor=FALSE, col=c("green","blue", "red", "yellow"))

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)

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> library(made4)
Loading required package: ade4
Loading required package: RColorBrewer
Loading required package: gplots

Attaching package: 'gplots'

The following object is masked from 'package:stats':

    lowess

Loading required package: scatterplot3d
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/made4/between.graph.Rd_%03d_medium.png", width=480, height=480)
> ### Name: between.graph
> ### Title: Plot 1D graph of results from between group analysis
> ### Aliases: between.graph
> ### Keywords: multivariate hplot
> 
> ### ** Examples
> 
> data(khan)
> if (require(ade4, quiet = TRUE)) {
+ khan.bga<-bga(khan$train, khan$train.classes)
+ }
> 
> between.graph(khan.bga)
> between.graph(khan.bga, ax=2, lwd=3, cex=0.5, col=c("green","blue", "red", "yellow"))
> between.graph(khan.bga, ax=2,  hor=FALSE, col=c("green","blue", "red", "yellow"))
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>