plot.perf {mixOmics} | R Documentation |
Function to plot performance criteria, such as MSEP, RMSEP, R^2, Q^2 for s/PLS methods, and classification performance for supervised methods, as a function of the number of components.
## S3 method for class 'perf.spls.mthd' plot(x, criterion = "MSEP", xlab = "number of components", ylab = NULL, LimQ2 = 0.0975, LimQ2.col = "darkgrey", cTicks = NULL, layout = NULL, ...) ## S3 method for class 'perf.splsda.mthd' plot(x, dist = c("all","max.dist","centroids.dist","mahalanobis.dist"), measure = c("all","overall","BER"), col, xlab = NULL, ylab = NULL, overlay=c("all", "measure", "dist"), legend.position=c("vertical", "horizontal"), sd = TRUE, ...) ## S3 method for class 'perf.mint.splsda.mthd' plot(x, dist = c("all","max.dist","centroids.dist","mahalanobis.dist"), measure = c("all","overall","BER"), col, xlab = NULL, ylab = NULL, study = "global", overlay= c("all", "measure", "dist"), legend.position=c("vertical", "horizontal"), ...) ## S3 method for class 'perf.sgccda.mthd' plot(x, dist = c("all","max.dist","centroids.dist","mahalanobis.dist"), measure = c("all","overall","BER"), col, weighted = TRUE, xlab = NULL, ylab = NULL, overlay= c("all", "measure", "dist"), legend.position=c("vertical","horizontal"), sd = TRUE, ...)
x |
an |
criterion |
character string. What type of validation criterion to plot for
|
dist |
prediction method applied in |
measure |
Two misclassification measure are available: overall misclassification error |
col |
character (or symbol) color to be used, possibly vector. One color per distance |
weighted |
plot either the performance of the Majority vote or the Weighted vote. |
study |
Indicates which study-specific outputs to plot. A character vector containing some levels of |
overlay |
parameter to overlay graphs; if 'all', only one graph is shown with all outputs; if 'measure', a graph is shown per distance; if 'dist', a graph is shown per measure. |
legend.position |
position of the legend, one of "vertical" (only one column) or "horizontal" (two columns). |
xlab, ylab |
titles for x and y axes. Typically character strings,
but can be expressions (e.g., |
LimQ2 |
numeric value. Signification limit for the components in the model.
Default is |
LimQ2.col |
character string specifying the color for the |
cTicks |
integer vector. Axis tickmark locations for the used number of components.
Default is |
layout |
numeric vector of length two giving the number of rows and columns in a
multi panel display. If not specified, |
sd |
If 'nrepeat' was used in the call to 'perf', error bar shows the standard deviation if sd=TRUE |
... |
Further arguments sent to |
plot.perf
creates one plot for each response variable in the
model, laid out in a multi panel display. It uses xyplot
for
performing the actual plotting.
More details about the prediction distances in ?predict
and the supplemental material of the mixOmics article (Rohart et al. 2017).
none
Ignacio González, Florian Rohart, Francois Bartolo, Kim-Anh Lê Cao.
Rohart F, Gautier B, Singh A, Lê Cao K-A. mixOmics: an R package for 'omics feature selection and multiple data integration. PLoS Comput Biol 13(11): e1005752
pls
, spls
, plsda
, splsda
,
perf
.
require(lattice) ## validation for objects of class 'pls' or 'spls' data(liver.toxicity) X <- liver.toxicity$gene Y <- liver.toxicity$clinic liver.pls <- pls(X, Y, ncomp = 3) liver.perf <- perf(liver.pls, validation = "Mfold") plot(liver.perf, criterion = "R2", layout = c(2, 2)) ## Not run: ## validation for objects of class 'plsda' or 'splsda' data(breast.tumors) X <- breast.tumors$gene.exp # Y will be transformed as a factor in the function, # but we set it as a factor to set up the colors. Y <- as.factor(breast.tumors$sample$treatment) res <- splsda(X, Y, ncomp = 2, keepX = c(25, 25)) breast.perf <- perf(res, nrepeat = 5) plot(breast.perf) plot(breast.perf, col=1:3) plot(breast.perf, col=1:3, sd=FALSE) ## End(Not run)