plot.perf: Plot for model performance
In mixOmics: Omics Data Integration Project
Description
Usage
Arguments
Details
Value
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.pls.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.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.plsda.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.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.plsda.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.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.
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.
...
Further arguments sent to xyplot function.
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.
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).
sd
If 'nrepeat' was used in the call to 'perf', error bar shows the
standard deviation if sd=TRUE
study
Indicates which study-specific outputs to plot. A character
vector containing some levels of object$study, "all.partial" to plot
all studies or "global" is expected. Default to "global".
weighted
plot either the performance of the Majority vote or the
Weighted vote.
Details
plot.perf creates one plot for each response variable in the model,
laid out in a multi panel display. It uses xyplot for
performing the actual plotting.
More details about the prediction distances in ?predict and the
supplemental material of the mixOmics article (Rohart et al. 2017).
Value
none
Author(s)
Ignacio González, Florian Rohart, Francois Bartolo, Kim-Anh Lê Cao, Al J Abadi
References
Rohart F, Gautier B, Singh A, Lê Cao K-A. mixOmics: an R package for 'omics
feature selection and multiple data integration. PLoS Comput Biol 13(11):
e1005752
See Also
pls, spls, plsda,
splsda, perf.
Examples
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require(lattice)
## validation for objects of class 'pls' or 'spls'
data(liver.toxicity)
X <- liver.toxicity$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)
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 Nov. 8, 2020, 11:12 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 Value 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 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 | ## S3 method for class 'perf.pls.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.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.plsda.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.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.plsda.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.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 |
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, |
... |
Further arguments sent to |
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 |
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). |
sd |
If 'nrepeat' was used in the call to 'perf', error bar shows the standard deviation if sd=TRUE |
study |
Indicates which study-specific outputs to plot. A character
vector containing some levels of |
weighted |
plot either the performance of the Majority vote or the Weighted vote. |
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).
Value
none
Author(s)
Ignacio González, Florian Rohart, Francois Bartolo, Kim-Anh Lê Cao, Al J Abadi
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 | 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)
|
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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