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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

Run this code
## 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)

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