Nothing
Biplots in 1D"
In biplotEZ: EZ-to-Use Biplots
knitr::opts_chunk$set(
fig.height = 6, fig.width = 7,
collapse = TRUE,
comment = "#>"
)
library(biplotEZ)
This vignette illustrates how to create one-dimensional biplot. The biplotEZ vignette demonstrates many functions of the functions in the package. The vignette will serve as a supplement to the biplotEZ vignette.
One-dimensional PCA biplot
One-dimensional PCA biplots are obtained by specifying dim.biplot = 1 in the call to PCA().
The one-dimensional representation of the data is displayed by the colour points on the top horizontal line. The accompanying calibrated variable axes are displayed as horizontal lines below. The variable name is displayed on the side to which the variable increases.
biplot(iris) |> PCA(group.aes = iris$Species,dim.biplot = 1) |> plot()
One-dimensional CVA biplot
Similarly for a CVA 1d biplot, dim.biplot = 1 is specified in the call to CVA(). The one-dimensioal CVA biplot displays the one-dimensional linear combination that maximises the between class variance, relative to the within class variance.
biplot(iris) |> CVA(classes = iris$Species,dim.biplot = 1) |>
axes(col="black") |> plot()
Classification using classify()
CVA models can be employed as a classifier. New observations are classified to the nearest class mean, where the means are indicated by the shaded squares on the scatter line. The classification regions are displayed above the scatter line using classify().
bp <- biplot(iris) |> CVA(classes = iris[,5],dim.biplot = 1)|>
axes(col="black") |>
classify(borders = TRUE,opacity = 1)|>plot()
The print() function provides the misclassification rate, as well as the confusion matrix, of the CVA classifier applied to the training data.
print(bp)
One-dimensional CA biplot
Similarly for a CA 1d biplot, dim.biplot = 1 is specified in the call to CA().
The one-dimensional biplot is constructed from the first columns of $\mathbf{U\Lambda^\gamma}$ and $&\mathbf{V\Lambda^{1-\gamma}}$.
Consider the HairEyeColor example again as discussed in CA in biplotEZ:
biplot(HairEyeColor[,,2], center = FALSE) |> CA(variant = "Princ",
dim.biplot=1, lambda.scal = T) |> plot()
The function interpolate()
interpolate() allows for new observations or axes to be added to the biplot.
The function newsamples()
The process of adding new samples to the biplot, called interpolation utilises the functions interpolate() and newsamples(). These functions work in the same way as in the call to the two-dimensional biplot. The function interpolate() accepts the argument newdata to specify a matrix or data frame containing the new samples to be interpolated. The function newsamples() operates the same way as samples() in that the user can specify the aesthetics of the interpolated samples.
biplot(iris[c(1:50,101:150),1:4])|> PCA(dim.biplot = 1) |> axes(col="black") |>
interpolate(newdata = iris[51:100,1:4]) |> newsamples(col="purple") |> plot()
The function newaxes()
To interpolate new variables to the biplot, the function interpolate() and newaxes() are called. The function interpolate() accepts the argument newvariable to specify a matrix or data frame of the same number of rows in the data specified in biplot() containing the new variables to be interpolated. The function newaxes() allows the user to specify the aesthetics of the interpolated variables.
biplot(iris[,1:3])|> PCA(dim.biplot = 1) |> axes(col="black") |>
interpolate(newvariable = iris[,4]) |>
newaxes(col="darkred",X.new.names = "Petal.Width") |> plot()
The function prediction()
Predicting Samples
To add the prediction of samples on the biplot, the prediction() function is used. The predict.samples argument takes in a vector indicating either the row numbers of the samples to predict or set to TRUE indicating to predict all samples. In the example below, the predictions for samples 100 to 150 are shown. The aesthetics for the display of the predictions are arguments in the axes() function: predict.col and predict.lwd.
biplot(iris) |>
PCA(group.aes = iris$Species,dim.biplot = 1,show.class.means = TRUE) |>
axes(col="black",predict.col = "darkred") |>
prediction(predict.samples=100:150) |> plot()
Predicting Group Means
Similarly, to add the prediction of group means, the function prediction() is used. The argument predict.means takes in a vector specifying which group means to predict. In the example below, only the first group means is predicted. Important to note that the argument show.class.means must be set to TRUE in the PCA() function.
biplot(iris) |>
PCA(group.aes = iris$Species,dim.biplot = 1,show.class.means = TRUE) |>
axes(col="black",predict.col = "darkred") |> means(label=TRUE,which=1:3)|>
prediction(predict.means = 1) |> plot()
Ellipses and Alpha bags
Ellipses are added to a 1d biplot using the ellipses() function which works in the same way as a 2d biplot. In one dimension concentration ellipses are simply a confidence interval. The concentration interval is indicated using rectangles spanning the range of the interval.
biplot(iris) |> PCA(group.aes = iris[,5],dim.biplot = 1) |>
axes(col="black") |>
ellipses() |> plot()
The one-dimensional representation of an Alpha bag will simply be an empirical interval. The empirical interval is indicated using rectangles spanning the range of the interval.
biplot(iris) |> PCA(group.aes = iris[,5],dim.biplot = 1) |>
axes(col="black") |>
alpha.bags(alpha = 0.7) |> plot()
The function density1D()
Overlapping points make the distribution of points on the scatter line difficult to identify. density1D() uses kernel density estimation (KDE), which adds a density plot to the one-dimensional biplot.
biplot(iris) |> PCA(dim.biplot = 1) |>
axes(col="black") |>
density1D() |> plot()
This KDE may be too smooth to display the distribution of the data. By changing the parameters of the KDE, we are able to address this issue. The bandwidth and kernel used in density1D() are controlled by the arguments h= and kernel=, respectively. The bandwidth h can take any positive value, see ?stats::density for more detail. kernel can take on any kernel supported by stats::density().
biplot(iris) |> PCA(dim.biplot = 1) |> axes(col='black') |>
density1D(h = 0.5 ,kernel = "triangular") |> plot()
The high concentration of observations in the right of the plot now becomes evident. To further explore the distributions of the observations, we may want to explore the density of groupings in the data. To do this, simply specify the group.aes= argument in PCA(). Here the density of the three species of iris is displayed.
biplot(iris) |> PCA(group.aes = iris[,5],dim.biplot = 1) |>
axes(col="black") |>
density1D() |> plot()
To only display the density of certain groups, use the which= argument in density1D().
biplot(iris) |> PCA(group.aes = iris[,5],dim.biplot = 1) |>
axes(col="black") |>
density1D(which = c(2,3)) |> plot()
The function legend.type()
legend.type adds a legend to the plot. A separate legend is created for each of the elements by setting each of samples, means, bags and ellipses equal to TRUE. Here, we add a legend for the samples.
biplot(iris) |> PCA(group.aes = iris[,5],dim.biplot = 1, show.class.means = TRUE) |>
axes(col="black") |> density1D() |> samples(opacity=0.5)|> alpha.bags()|>
legend.type(samples = TRUE) |> plot()
If other legends are added, they will overlap with the elements of the plot as displayed below.
biplot(iris) |> PCA(group.aes = iris[,5],dim.biplot = 1, show.class.means = TRUE) |>
axes(col="black") |> density1D() |> samples(opacity=0.5)|> alpha.bags()|>
legend.type(samples = TRUE,means = TRUE, bags = TRUE) |> plot()
By specifying new=TRUE, the legends will be displayed on a new plot.
biplot(iris) |> PCA(group.aes = iris[,5],dim.biplot = 1, show.class.means = TRUE) |>
axes(col="black") |> density1D() |> samples(opacity=0.5)|> alpha.bags()|>
legend.type(samples = TRUE,means = TRUE, bags = TRUE, new=TRUE) |> plot()
For the CVA biplot legend.type also displays a legend for classification regions if `
bp <- biplot(iris) |> CVA(classes = iris[,5],dim.biplot = 1, show.class.means = TRUE) |>
axes(col="black") |> classify() |> density1D() |> samples(opacity=0.5)|> alpha.bags()|>
legend.type(samples = TRUE,means = TRUE, bags = TRUE, regions = TRUE, new=TRUE) |> plot() #
The function fit.measures()
fit.measures() calculates measures of fit for the biplot. Passing a biplot object which has been piped to fit.measures() to summary() will output:
- For the plot: Quality of fit.
- For each variable: an Adequacy measure and a measure of Axis Predictivity.
- For each sample: Sample Predictivity
a <- biplot(iris) |> PCA(group.aes = iris[,5],dim.biplot = 1) |> fit.measures()
summary(a)
References
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biplotEZ documentation built on April 4, 2025, 2:20 a.m.
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
knitr::opts_chunk$set( fig.height = 6, fig.width = 7, collapse = TRUE, comment = "#>" )
library(biplotEZ)
This vignette illustrates how to create one-dimensional biplot. The biplotEZ vignette demonstrates many functions of the functions in the package. The vignette will serve as a supplement to the biplotEZ vignette.
One-dimensional PCA biplot
One-dimensional PCA biplots are obtained by specifying dim.biplot = 1 in the call to PCA().
The one-dimensional representation of the data is displayed by the colour points on the top horizontal line. The accompanying calibrated variable axes are displayed as horizontal lines below. The variable name is displayed on the side to which the variable increases.
biplot(iris) |> PCA(group.aes = iris$Species,dim.biplot = 1) |> plot()
One-dimensional CVA biplot
Similarly for a CVA 1d biplot, dim.biplot = 1 is specified in the call to CVA(). The one-dimensioal CVA biplot displays the one-dimensional linear combination that maximises the between class variance, relative to the within class variance.
biplot(iris) |> CVA(classes = iris$Species,dim.biplot = 1) |> axes(col="black") |> plot()
Classification using classify()
CVA models can be employed as a classifier. New observations are classified to the nearest class mean, where the means are indicated by the shaded squares on the scatter line. The classification regions are displayed above the scatter line using classify().
bp <- biplot(iris) |> CVA(classes = iris[,5],dim.biplot = 1)|> axes(col="black") |> classify(borders = TRUE,opacity = 1)|>plot()
The print() function provides the misclassification rate, as well as the confusion matrix, of the CVA classifier applied to the training data.
print(bp)
One-dimensional CA biplot
Similarly for a CA 1d biplot, dim.biplot = 1 is specified in the call to CA().
The one-dimensional biplot is constructed from the first columns of $\mathbf{U\Lambda^\gamma}$ and $&\mathbf{V\Lambda^{1-\gamma}}$.
Consider the HairEyeColor example again as discussed in CA in biplotEZ:
biplot(HairEyeColor[,,2], center = FALSE) |> CA(variant = "Princ", dim.biplot=1, lambda.scal = T) |> plot()
The function interpolate()
interpolate() allows for new observations or axes to be added to the biplot.
The function newsamples()
The process of adding new samples to the biplot, called interpolation utilises the functions interpolate() and newsamples(). These functions work in the same way as in the call to the two-dimensional biplot. The function interpolate() accepts the argument newdata to specify a matrix or data frame containing the new samples to be interpolated. The function newsamples() operates the same way as samples() in that the user can specify the aesthetics of the interpolated samples.
biplot(iris[c(1:50,101:150),1:4])|> PCA(dim.biplot = 1) |> axes(col="black") |> interpolate(newdata = iris[51:100,1:4]) |> newsamples(col="purple") |> plot()
The function newaxes()
To interpolate new variables to the biplot, the function interpolate() and newaxes() are called. The function interpolate() accepts the argument newvariable to specify a matrix or data frame of the same number of rows in the data specified in biplot() containing the new variables to be interpolated. The function newaxes() allows the user to specify the aesthetics of the interpolated variables.
biplot(iris[,1:3])|> PCA(dim.biplot = 1) |> axes(col="black") |> interpolate(newvariable = iris[,4]) |> newaxes(col="darkred",X.new.names = "Petal.Width") |> plot()
The function prediction()
Predicting Samples
To add the prediction of samples on the biplot, the prediction() function is used. The predict.samples argument takes in a vector indicating either the row numbers of the samples to predict or set to TRUE indicating to predict all samples. In the example below, the predictions for samples 100 to 150 are shown. The aesthetics for the display of the predictions are arguments in the axes() function: predict.col and predict.lwd.
biplot(iris) |> PCA(group.aes = iris$Species,dim.biplot = 1,show.class.means = TRUE) |> axes(col="black",predict.col = "darkred") |> prediction(predict.samples=100:150) |> plot()
Predicting Group Means
Similarly, to add the prediction of group means, the function prediction() is used. The argument predict.means takes in a vector specifying which group means to predict. In the example below, only the first group means is predicted. Important to note that the argument show.class.means must be set to TRUE in the PCA() function.
biplot(iris) |> PCA(group.aes = iris$Species,dim.biplot = 1,show.class.means = TRUE) |> axes(col="black",predict.col = "darkred") |> means(label=TRUE,which=1:3)|> prediction(predict.means = 1) |> plot()
Ellipses and Alpha bags
Ellipses are added to a 1d biplot using the ellipses() function which works in the same way as a 2d biplot. In one dimension concentration ellipses are simply a confidence interval. The concentration interval is indicated using rectangles spanning the range of the interval.
biplot(iris) |> PCA(group.aes = iris[,5],dim.biplot = 1) |> axes(col="black") |> ellipses() |> plot()
The one-dimensional representation of an Alpha bag will simply be an empirical interval. The empirical interval is indicated using rectangles spanning the range of the interval.
biplot(iris) |> PCA(group.aes = iris[,5],dim.biplot = 1) |> axes(col="black") |> alpha.bags(alpha = 0.7) |> plot()
The function density1D()
Overlapping points make the distribution of points on the scatter line difficult to identify. density1D() uses kernel density estimation (KDE), which adds a density plot to the one-dimensional biplot.
biplot(iris) |> PCA(dim.biplot = 1) |> axes(col="black") |> density1D() |> plot()
This KDE may be too smooth to display the distribution of the data. By changing the parameters of the KDE, we are able to address this issue. The bandwidth and kernel used in density1D() are controlled by the arguments h= and kernel=, respectively. The bandwidth h can take any positive value, see ?stats::density for more detail. kernel can take on any kernel supported by stats::density().
biplot(iris) |> PCA(dim.biplot = 1) |> axes(col='black') |> density1D(h = 0.5 ,kernel = "triangular") |> plot()
The high concentration of observations in the right of the plot now becomes evident. To further explore the distributions of the observations, we may want to explore the density of groupings in the data. To do this, simply specify the group.aes= argument in PCA(). Here the density of the three species of iris is displayed.
biplot(iris) |> PCA(group.aes = iris[,5],dim.biplot = 1) |> axes(col="black") |> density1D() |> plot()
To only display the density of certain groups, use the which= argument in density1D().
biplot(iris) |> PCA(group.aes = iris[,5],dim.biplot = 1) |> axes(col="black") |> density1D(which = c(2,3)) |> plot()
The function legend.type()
legend.type adds a legend to the plot. A separate legend is created for each of the elements by setting each of samples, means, bags and ellipses equal to TRUE. Here, we add a legend for the samples.
biplot(iris) |> PCA(group.aes = iris[,5],dim.biplot = 1, show.class.means = TRUE) |> axes(col="black") |> density1D() |> samples(opacity=0.5)|> alpha.bags()|> legend.type(samples = TRUE) |> plot()
If other legends are added, they will overlap with the elements of the plot as displayed below.
biplot(iris) |> PCA(group.aes = iris[,5],dim.biplot = 1, show.class.means = TRUE) |> axes(col="black") |> density1D() |> samples(opacity=0.5)|> alpha.bags()|> legend.type(samples = TRUE,means = TRUE, bags = TRUE) |> plot()
By specifying new=TRUE, the legends will be displayed on a new plot.
biplot(iris) |> PCA(group.aes = iris[,5],dim.biplot = 1, show.class.means = TRUE) |> axes(col="black") |> density1D() |> samples(opacity=0.5)|> alpha.bags()|> legend.type(samples = TRUE,means = TRUE, bags = TRUE, new=TRUE) |> plot()
For the CVA biplot legend.type also displays a legend for classification regions if `
bp <- biplot(iris) |> CVA(classes = iris[,5],dim.biplot = 1, show.class.means = TRUE) |> axes(col="black") |> classify() |> density1D() |> samples(opacity=0.5)|> alpha.bags()|> legend.type(samples = TRUE,means = TRUE, bags = TRUE, regions = TRUE, new=TRUE) |> plot() #
The function fit.measures()
fit.measures() calculates measures of fit for the biplot. Passing a biplot object which has been piped to fit.measures() to summary() will output:
- For the plot: Quality of fit.
- For each variable: an Adequacy measure and a measure of Axis Predictivity.
- For each sample: Sample Predictivity
a <- biplot(iris) |> PCA(group.aes = iris[,5],dim.biplot = 1) |> fit.measures() summary(a)
References
Try the biplotEZ package in your browser
Any scripts or data that you put into this service are public.
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.
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