| s.match {integrOmics} | R Documentation |
performs the scatter diagram for a paired coordinates.
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)
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. |
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.
The matched call.
Daniel Chessel from ade4 R package, modified by Kim-Anh Lê Cao.
Lê Cao, K.-A., Martin, P.G.P., Robert-Granié, C. and Besse, P. (2009). Sparse canonical methods for biological data integration: application to a cross-platform study. BMC Bioinformatics 10:34.
## 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)