s.var: Draw xy plots of results of multivariate analysis

In SamGG/made4: Multivariate analysis of microarray data using ADE4

Description

A number of functions for graphically displaying results from between group, coinertia, or other multivariate analysis of gene expression data. s.var, s.groups and s.match.col are derived from ADE4 graphics modules, s.label, s.class and s.match respectively.

Usage

s.var(dfxy, xax = 1, yax = 2, label = row.names(dfxy), clabel = 1, pch = 20, 
      cpoint = if (clabel == 0) 1 else 0, neig = NULL, cneig = 2, xlim = NULL, 
      ylim = NULL, grid = TRUE, addaxes = TRUE, cgrid = 1, include.origin = TRUE, 
      origin = c(0, 0), sub = "", csub = 1.25, possub = "bottomleft", pixmap = NULL, 
      contour = NULL, area = NULL, add.plot = FALSE, colpoints = rep(1, nrow(dfxy)), 
      boxes = TRUE, ...)
s.groups(dfxy, classvec, wt = rep(1, length(classvec)), xax = 1, yax = 2, cstar = 1,
      cellipse = 1.5, axesell = TRUE, label = levels(classvec), slabel = row.names(dfxy),
      clabel = 1, cpoint = 1, pch = 20, col = rep(1, length(levels(classvec))),
      xlim = NULL, ylim = NULL, grid = TRUE, addaxes = TRUE, origin = c(0, 0), 
      include.origin = TRUE, sub = "", csub = 1, possub = "bottomleft", 
      cgrid = 1, pixmap = NULL, contour = NULL, area = NULL, add.plot = FALSE, ...)
s.match.col(df1xy, df2xy, xax = 1, yax = 2, pch = 20, cpoint = 1, 
      label = row.names(df1xy), clabel = 1, edge = TRUE, xlim = NULL, ylim = NULL, 
      grid = TRUE, addaxes = TRUE, cgrid = 1, include.origin = TRUE, origin = c(0, 0), 
      sub = "", csub = 1.25, possub = "bottomleft", pixmap = NULL, contour = NULL, 
      area = NULL, add.plot = FALSE, col = rep(1, nrow(df1xy)), classvec=NULL,...)

Arguments

dfxy	coordinates, normally the \$ls, \$co or \$li coordinates from PCA, COA or BGA with at least two columns, containing the x,y coordinates to be plotted
df1xy, df2xy	coordinates from cia, normally the \$mX, \$mY coordinates with at least two columns, containing the x,y coordinates to be plotted
colpoints	Character, colour of arrays (cases),genes or points
xax	the column number for the x-axis
yax	the column number for the y-axis
classvec	Factor. A factor, classvec partitioning the rows of the data frame in classes
boxes	A logical, indicating whether a box should be drawn around each variable label. The default is TRUE
add.plot	logical if TRUE plot draw in current graphics window
origin, sub, wt, cstar, cellipse, axesell, col, edge	Graphing parameters. See s.label or s.class for details
clabel,pch, cpoint, neig, cneig, xlim, ylim, grid, addaxes, cgrid, include.origin, csub, possub, pixmap, contour, area	Graphing parameters, see s.match for details
...	further arguments passed to or from other method

Details

These functions are modified versions of s.label, s.class and s.match graph modules from ADE4. Please see s.label or s.class and s.match for father details.

These functions s.var, s.groups and s.match.col are called by plot.bga and plot.cia.

Author(s)

Aedin Culhane

See Also

See also s.class, s.label, s.match

Examples

data(khan)
if (require(ade4, quiet = TRUE)) {
khan.bga<-bga(khan$train, khan$train.classes)
attach(khan.bga)
par(mfrow=c(2,2))
s.var(bet$ls, col=as.numeric(khan$train.classes), clabel=0.8)
s.groups(bet$ls, khan$train.classes, add.plot=TRUE, 
col=c(1:length(levels(khan$train.classes))) )

}

SamGG/made4 documentation built on Sept. 29, 2020, 1:33 p.m.