| Title: | A ggplot2 based biplot |
|---|---|
| Description: | A ggplot2 based biplot. It provides a drop-in replacement for biplot.princomp(). It implements a biplot and scree plot using ggplot2. |
| Authors: | Vincent Q. Vu <[email protected]> |
| Maintainer: | Vincent Q. Vu <[email protected]> |
| License: | GPL-2 |
| Version: | 0.55 |
| Built: | 2025-03-14 04:44:09 UTC |
| Source: | https://github.com/vqv/ggbiplot |
Biplot for Principal Components using ggplot2
ggbiplot(pcobj, choices = 1:2, scale = 1, pc.biplot = TRUE, obs.scale = 1 - scale, var.scale = scale, groups = NULL, ellipse = FALSE, ellipse.prob = 0.68, labels = NULL, labels.size = 3, alpha = 1, var.axes = TRUE, circle = FALSE, circle.prob = 0.69, varname.size = 3, varname.adjust = 1.5, varname.abbrev = FALSE, ...)ggbiplot(pcobj, choices = 1:2, scale = 1, pc.biplot = TRUE, obs.scale = 1 - scale, var.scale = scale, groups = NULL, ellipse = FALSE, ellipse.prob = 0.68, labels = NULL, labels.size = 3, alpha = 1, var.axes = TRUE, circle = FALSE, circle.prob = 0.69, varname.size = 3, varname.adjust = 1.5, varname.abbrev = FALSE, ...)
pcobj |
an object returned by prcomp() or princomp() |
choices |
which PCs to plot |
scale |
covariance biplot (scale = 1), form biplot (scale = 0). When scale = 1, the inner product between the variables approximates the covariance and the distance between the points approximates the Mahalanobis distance. |
obs.scale |
scale factor to apply to observations |
var.scale |
scale factor to apply to variables |
pc.biplot |
for compatibility with biplot.princomp() |
groups |
optional factor variable indicating the groups that the observations belong to. If provided the points will be colored according to groups |
ellipse |
draw a normal data ellipse for each group? |
ellipse.prob |
size of the ellipse in Normal probability |
labels |
optional vector of labels for the observations |
labels.size |
size of the text used for the labels |
alpha |
alpha transparency value for the points (0 = TRUEransparent, 1 = opaque) |
circle |
draw a correlation circle? (only applies when prcomp was called with scale = TRUE and when var.scale = 1) |
var.axes |
draw arrows for the variables? |
varname.size |
size of the text for variable names |
varname.adjust |
adjustment factor the placement of the variable names, >= 1 means farther from the arrow |
varname.abbrev |
whether or not to abbreviate the variable names |
a ggplot2 plot
data(wine) wine.pca <- prcomp(wine, scale. = TRUE) print(ggbiplot(wine.pca, obs.scale = 1, var.scale = 1, groups = wine.class, ellipse = TRUE, circle = TRUE))data(wine) wine.pca <- prcomp(wine, scale. = TRUE) print(ggbiplot(wine.pca, obs.scale = 1, var.scale = 1, groups = wine.class, ellipse = TRUE, circle = TRUE))
Screeplot for Principal Components
ggscreeplot(pcobj, type = c("pev", "cev"))ggscreeplot(pcobj, type = c("pev", "cev"))
pcobj |
an object returned by prcomp() or princomp() |
type |
the type of scree plot. 'pev' corresponds proportion of explained variance, i.e. the eigenvalues divided by the trace. 'cev' corresponds to the cumulative proportion of explained variance, i.e. the partial sum of the first k eigenvalues divided by the trace. |
data(wine) wine.pca <- prcomp(wine, scale. = TRUE) print(ggscreeplot(wine.pca))data(wine) wine.pca <- prcomp(wine, scale. = TRUE) print(ggscreeplot(wine.pca))
Chemical constituents of wines from three different cultivars grown in the same region in Italy. The cultivars, 'barolo', 'barbera', and 'grignolino', are indicated in wine.class.
data(wine)data(wine)
The format is: chr "wine"
http://archive.ics.uci.edu/ml/datasets/Wine
data(wine) wine.pca <- prcomp(wine, scale. = TRUE) print(ggscreeplot(wine.pca)) print(ggbiplot(wine.pca, obs.scale = 1, var.scale = 1, groups = wine.class, ellipse = TRUE, circle = TRUE))data(wine) wine.pca <- prcomp(wine, scale. = TRUE) print(ggscreeplot(wine.pca)) print(ggbiplot(wine.pca, obs.scale = 1, var.scale = 1, groups = wine.class, ellipse = TRUE, circle = TRUE))