plot.perf: Plot for model performance
In mixOmics: Omics Data Integration Project
Description
Usage
Arguments
Details
Author(s)
References
See Also
Examples
Description
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.
Usage
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## 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,
...)
Arguments
x
an perf object.
criterion
character string. What type of validation criterion to plot for
pls or spls. One of "MSEP", "RMSEP", "R2" or "Q2".
See perf.
dist
prediction method applied in perf for plsda or splsda.
See perf.
measure
Two misclassification measure are available: overall misclassification error overall or the Balanced Error Rate BER
col
character (or symbol) color to be used, possibly vector. One color per distance dist.
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 object$study, "all.partial" to plot all studies or "global" is expected. Default to "global".
overlay
parameter to overlay graphs; if 'all', only one graph is shown with all outputs; if 'measure', a graph is shown per distance; if 'dist', a graph is shown per measure.
legend.position
position of the legend, one of "vertical" (only one column) or "horizontal" (two columns).
xlab, ylab
titles for x and y axes. Typically character strings,
but can be expressions (e.g., expression(R^2)).
LimQ2
numeric value. Signification limit for the components in the model.
Default is LimQ2 = 0.0975.
LimQ2.col
character string specifying the color for the LimQ2 line to be plotted.
If "none" the line will not be plotted.
cTicks
integer vector. Axis tickmark locations for the used number of components.
Default is 1:ncomp (see perf).
layout
numeric vector of length two giving the number of rows and columns in a
multi panel display. If not specified, plot.perf tries to be intelligent.
sd
If 'nrepeat' was used in the call to 'perf', error bar shows the standard deviation if sd=TRUE
...
Further arguments sent to xyplot function.
Details
plot.perf creates one plot for each response variable in the
model, laid out in a multi panel display. It uses xyplot for
performing the actual plotting.
More details about the prediction distances in ?predict and the supplemental material of the mixOmics article (Rohart et al. 2017).
Author(s)
Ignacio González, Florian Rohart, Francois Bartolo, Kim-Anh Lê Cao.
References
Rohart F, Gautier B, Singh A, Lê Cao K-A. mixOmics: an R package for 'omics feature selection and multiple data integration. PLoS Comput Biol 13(11): e1005752
See Also
pls, spls, plsda, splsda,
perf.
Examples
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require(lattice)
## validation for objects of class 'pls' or 'spls'
## Not run:
data(liver.toxicity)
X <- liver.toxicity$gene
Y <- liver.toxicity$clinic
liver.pls <- pls(X, Y, ncomp = 3)
liver.perf <- perf(liver.pls, validation = "Mfold")
plot(liver.perf, criterion = "R2", layout = c(2, 2))
## End(Not run)
## validation for objects of class 'plsda' or 'splsda'
## Not run:
data(breast.tumors)
X <- breast.tumors$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)
Example output
Loading required package: MASS
Loading required package: lattice
Loading required package: ggplot2
Loaded mixOmics 6.3.2
Thank you for using mixOmics!
How to apply our methods: http://www.mixOmics.org for some examples.
Questions or comments: email us at mixomics[at]math.univ-toulouse.fr
Any bugs? https://bitbucket.org/klecao/package-mixomics/issues
Cite us: citation('mixOmics')
Warning messages:
1: In rgl.init(initValue, onlyNULL) : RGL: unable to open X11 display
2: 'rgl_init' failed, running with rgl.useNULL = TRUE
3: .onUnload failed in unloadNamespace() for 'rgl', details:
call: fun(...)
error: object 'rgl_quit' not found
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mixOmics documentation built on June 1, 2018, 5:06 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Description Usage Arguments Details Author(s) References See Also Examples
Description
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.
Usage
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 | ## 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,
...)
|
Arguments
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 |
Details
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).
Author(s)
Ignacio González, Florian Rohart, Francois Bartolo, Kim-Anh Lê Cao.
References
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
See Also
pls, spls, plsda, splsda,
perf.
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 | require(lattice)
## validation for objects of class 'pls' or 'spls'
## Not run:
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))
## End(Not run)
## validation for objects of class 'plsda' or 'splsda'
## Not run:
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)
|
Example output
Loading required package: MASS
Loading required package: lattice
Loading required package: ggplot2
Loaded mixOmics 6.3.2
Thank you for using mixOmics!
How to apply our methods: http://www.mixOmics.org for some examples.
Questions or comments: email us at mixomics[at]math.univ-toulouse.fr
Any bugs? https://bitbucket.org/klecao/package-mixomics/issues
Cite us: citation('mixOmics')
Warning messages:
1: In rgl.init(initValue, onlyNULL) : RGL: unable to open X11 display
2: 'rgl_init' failed, running with rgl.useNULL = TRUE
3: .onUnload failed in unloadNamespace() for 'rgl', details:
call: fun(...)
error: object 'rgl_quit' not found
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