mixOmics (version 5.1.2)

s.match: Plot of Paired Coordinates

Description

performs the scatter diagram for a paired coordinates.

Usage

s.match(df1xy, df2xy, xax = 1, yax = 2, pch = 20, cpoint = 1, 
        label = row.names(df1xy), clabel = 1, edge = TRUE, 
        xlim = NULL, ylim = NULL, grid = FALSE, 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, lty = 1)

Arguments

df1xy

a data frame containing two columns from the first system.

df2xy

a data frame containing two columns from the second system.

xax

the column number for the $x$-axis of both the two systems.

yax

the column number for the $y$-axis of both the two systems.

pch

if cpoint $> 0$, an integer specifying the symbol or the single character to be used in plotting points.

cpoint

a character size for plotting the points, used with par("cex")*cpoint. If zero, no points are drawn.

label

a vector of strings of characters for the couple labels.

clabel

if not NULL, a character size for the labels, used with par("cex")*clabel.

edge

if TRUE the arrows are plotted, otherwise only the segments are drawn.

xlim

the ranges to be encompassed by the $x$ axis, if NULL they are computed.

ylim

the ranges to be encompassed by the $y$ axis, if NULL they are computed.

grid

a logical value indicating whether a grid in the background of the plot should be drawn.

addaxes

a logical value indicating whether the axes should be plotted.

cgrid

a character size, parameter used with par("cex")*cgrid to indicate the mesh of the grid.

include.origin

a logical value indicating whether the point "origin" should be belonged to the graph space.

origin

the fixed point in the graph space, for example c(0,0) the origin axes.

sub

a string of characters to be inserted as legend.

csub

a character size for the legend, used with par("cex")*csub.

possub

character string indicating the sub-title position ("topleft", "topright", "bottomleft", "bottomright").

pixmap

an object pixmap displayed in the map background.

contour

a data frame with 4 columns to plot the contour of the map : each row gives a segment (x1, y1, x2, y2).

area

a data frame of class 'area' to plot a set of surface units in contour.

add.plot

if TRUE uses the current graphics window.

col

vector of size n (the number of samples) to indicate the biological conditions of each sample.

lty

set by default to 1.

Value

• The matched call.

encoding

latin1

Details

Graphical of the samples (individuals) is displayed in a superimposed manner where each sample will be indicated using an arrow. The start of the arrow indicates the location of the sample in $X$ in one plot, and the tip the location of the sample in $Y$ in the other plot. Short arrows indicate if both data sets strongly agree and long arrows a disagreement between the two data sets.

References

Le Cao, K.-A., Martin, P.G.P., Robert-Granie, C. and Besse, P. (2009). Sparse canonical methods for biological data integration: application to a cross-platform study. BMC Bioinformatics 10:34.

Examples

## relevant only for canonical mode
data(liver.toxicity)
X <- liver.toxicity$gene
Y <- liver.toxicity$clinic
toxicity.spls <- spls(X, Y, mode = "canonical", ncomp = 3, 
                      keepX = c(50, 50, 50), keepY = c(10, 10, 10))

color.toxicity <- as.numeric(liver.toxicity$treatment[, 2])
label.toxicity <- liver.toxicity$treatment[, 1]
s.match(toxicity.spls$variates$X[, c(1, 2)], 
        toxicity.spls$variates$Y[, c(1, 2)], 
        clabel = 0.5, label = label.toxicity, col = color.toxicity)