s.var {made4} | R Documentation |
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.
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,...)
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, $mY
coordinates with at least two columns, containing the x,y coordinates to
be plotted |
colpoints |
Character, colour of arrays (cases),genes or points |
xax |
the column number for the x-axis |
yax |
the column number for the y-axis |
classvec |
Factor . A factor, classvec partitioning the rows of the data
frame in classes |
boxes |
A logical, indicating whether a box should be drawn around each variable label. The default is TRUE |
add.plot |
logical if TRUE plot draw in current graphics window |
origin, sub, wt, cstar, cellipse, axesell,
col, edge |
Graphing parameters. See s.label or s.class
for details |
clabel,pch, cpoint, neig, cneig, xlim, ylim, grid,
addaxes, cgrid, include.origin, csub, possub, pixmap, contour,
area |
Graphing parameters, see s.match for details |
... |
further arguments passed to or from other method |
These functions are modified versions of s.label, s.class and s.match graph
modules from ADE4. Please see s.label
or
s.class
and s.match
for father details.
These functions s.var
, s.groups
and s.match.col
are called by
plot.bga
and plot.cia
.
Aedin Culhane
See also s.class
,
s.label
,
s.match
data(khan) if (require(ade4, quiet = TRUE)) { khan.bga<-bga(khan$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))) ) }