plot.mpm {mpm} | R Documentation |
Produces a spectral map plot (biplot) of an object of class mpm
## S3 method for class 'mpm': plot(x, scale = c("singul", "eigen", "uvr", "uvc"), dim = c(1, 2), zoom = rep(1, 2), show.row = c("all", "position"), show.col = c("all", "position"), col.group = rep(1, length(x$col.names)), colors = c("orange1", "red", rainbow(length(unique(col.group)), start = 2/6, end = 4/6)), col.areas = TRUE , col.symbols = c(1, rep(2, length(unique(col.group)))), rot = rep(-1, length(dim)), labels = NULL, label.tol = 1, lab.size = 0.725, col.size = 10, row.size = 10, do.smoothScatter = FALSE, do.plot = TRUE, ...)
x |
object of class mpm a result of a call to mpm . |
scale |
optional character string specifying the type of factor
scaling of the biplot. This can be either \dQuote{singul}
(singular value scaling), \dQuote{eigen} (eigenvalue scaling),
\dQuote{uvr} (unit row-variance scaling), \dQuote{uvc}
(unit column-variance scaling). The latter is of particular value
when analyzing large matrices, such as gene expression
data. Singular value scaling \dQuote{singul} is customary in
spectral map analysis. Defaults to \dQuote{singul} . |
dim |
optional principal factors that are plotted along the
horizontal and vertical axis. Defaults to c(1,2) . |
zoom |
optional zoom factor for row and column items. Defaults to
c(1,1) . |
show.row |
optional character string indicating whether all rows
(\dQuote{all} ) are to be plotted or just the positioned rows
\dQuote{position} . |
show.col |
optional character string indicating whether all
columns (\dQuote{all} ) are to be plotted or just the
positioned columns \dQuote{position} . |
col.group |
optional vector (character or numeric) indicating the
different groupings of the columns, e.g. Golub.grp . Defaults to 1. |
colors |
vector specifying the colors for the annotation of the plot; the first two elements concern the rows; the third till the last element concern the columns; the first element will be used to color the unlabeled rows; the second element for the labeled rows and the remaining elements to give different colors to different groups of columns. |
col.areas |
logical value indicating whether columns should be
plotted as squares with areas proportional to their marginal mean
and colors representing the different groups (TRUE ), or with
symbols representing the groupings and identical size
(FALSE ). Defaults to TRUE . |
col.symbols |
vector of symbols when col.areas=FALSE
corresponds to the pch argument of the function plot . |
rot |
rotation of plot. Defaults to c(-1,-1) . |
labels |
character vector to be used for labeling points on the graph;
if NULL , the row names of x are used instead |
label.tol |
numerical value specifying either the percentile
(label.tol<=1 )of rows or the number of rows
(label.tol>1 ) most distant from the plot-center (0,0) that
are labeled and are plotted as circles with area proportional to the
marginal means of the original data. |
lab.size |
size of identifying labels for row- and column-items
as cex parameter of the text function |
col.size |
size in mm of the column symbols |
row.size |
size in mm of the row symbols |
do.smoothScatter |
use smoothScatter or not instead of plotting individual points |
do.plot |
produce a plot or not |
... |
further arguments to eqscaleplot which draws the canvas
for the plot; useful for adding a main or a custom sub |
Spectral maps are special types of biplots with the area of the symbols
proportional to some measure, usually the row or column mean value and
an identification of row- and column-items.
For large matrices, such as gene expression data, where there is an
abundance of rows, this can obscure the plot.
In this case, the argument label.tol
can be used to select the
most informative rows, i.e. rows that are most distant from the center of the plot.
Only these row-items are then labeled and represented as circles with
their areas proportional to the marginal mean value.
For the column-items it can be useful to apply some grouping specified
by col.group
. Examples of groupings are different pathologies,
such as specified in Golub.grp
An object of class plot.mpm
that has the following components:
Rows |
a data frame with the X and Y coordinates of the rows and
an indication Select of whether the row was selected
according to label.tol |
Columns |
a data frame with the X and Y coordinates of the columns |
Requires the package MASS
to be present
value
is returned invisibly, but is available for further
use when an explicit assignment is made
Luc Wouters
Wouters, L., Goehlmann, H., Bijnens, L., Kass, S.U., Molenberghs, G., Lewi, P.J. (2003). Graphical exploration of gene expression data: a comparative study of three multivariate methods. Biometrics 59, 1131-1140.
# Weighted spectral map analysis data(Golub) # Gene expression data of leukemia patients data(Golub.grp) # Pathological classes coded as 1, 2, 3 r.sma <- mpm(Golub[,1:39], row.weight = "mean", col.weight = "mean") # Spectral map biplot with result r <- plot(r.sma, label.tol = 20, scale = "uvc", col.group = (Golub.grp)[1:38], zoom = c(1,1.2), col.size = 5) Golub[r$Rows$Select, 1] # 20 most extreme genes