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Questions tagged [ggbiplot]

A biplot based on ggplot2.

This tag refer to the library ggbiplot on github for the programming language. One can install it with:

library(devtools)
install_github("vqv/ggbiplot")

It allows to plot Principal Component Analysis using ggplot (see ).

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Adding subscripts to the variable names of a PCA using ggbiplot?

I have the following PCA plot with 7 variables (see data and code below), where I want the variable names to be put in subscript. In ggbiplot() however, the variable names are automatically taken from the column names of the matrix that was used to…
Jonas Coussement
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Principal Component Analysis in R, ggbiplot

I'm a biologist trying to use R, and I'm struggling with it. I'm trying to generate a Principal Component Analysis for this…
Camile Castilho Fontelles
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Supplementary variables in ggbiplot PCA

I am trying to draw PCA results with ggbiplot, how can I draw supplementary variables ? I found this discussion for MCA results, but I would like to have the arrows as well... data(wine) wine.pca <- PCA(wine, scale. = TRUE, quanti.sup = c(4,5)) …
Nausi
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How to adjust ellipses overlap calculation in overlap{siar} to match normal probability ellipsoids in ggbiplot?

Going back to this thread, I was calculating the intersection between two ellipses e.g. the volume of the intersection between versicolor and virginca: using the following mwe: data(iris) log.ir <- log(iris[, 1:4]) ir.species <- iris[, 5] ir.pca <-…
raumkundschafter
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How to bind/merge prcomp and predict data in r?

To plot a predicted validation/test data set within a training dataset in ggbiplot as addressed here, I would like to bind/merge the two datasets. The given mwe is: library(ggbiplot) data(wine) ##pca on the wine dataset used as training…
raumkundschafter
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Error while installing ggbiplot - object 'digest_impl' not found

When installing ggbiplot I get the following error: > library(devtools) > install_github("vqv/ggbiplot") Downloading GitHub repo vqv/ggbiplot@master from URL https://api.github.com/repos/vqv/ggbiplot/zipball/master Installing ggbiplot Error in…
Mark
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in R, how to install ggbiplot?

I am running R version 3.2.3 in RStudio. I tried following these instructions: library(devtools) install_github("ggbiplot", "vqv") and library(devtools) install_github("vqv/ggbiplot") from here http://www.vince.vu/software/ but I am getting this…
val
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ggbiplot graphical display in groups

I am learning biplot with wine data set. How does R know Barolo, Grignolino and Barbera are wine.class while we don't see the wine class column in the data set? More details about the wine data set are in the following links ggbiplot - how not to…
Little Bee
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ggbiplots - PCA: colour and shape of points according to groups

I have modified the iris data to provide an example of what I would like to do. I add an extra column to the iris data as provided in the link below. This extra column has also some groups based on organs. I then do the PCA and plot it. I would like…
Paul
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how to make the biplot name more clear using ggbiplot

I have a data which can be download from here https://gist.github.com/anonymous/5f1135e4f750a39b0255 I try to plot a PCA with ggbiplot using the following function data <- read.delim("path to the data.txt") data.pca <- prcomp (data, center = TRUE,…
Best
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R: Plot a subset of principal component variables when you have too many variables

I am new to using Vegan for ecosystem level analysis. I have a dataset with over 4,000 taxa across ten sites, and another with 37 chem-based observations from all ten sites. I have analyzed both sets of data using prcomp from the Vegan package,…
Ina.Quest
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ggbiplot for R version 3.1.0

I'm trying to install ggbiplot on the version 3.1.0 of R from Github I get a warning message saying the package isn't available for R version 3.1.0. Am I downloading the wring version of ggbiplot? Is there a newer version? Where? Or am I simply…
Liza Roger
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ggbiplot groups colour scale to be discrete

In the wine data examples the scatterplot has groups in discrete colours, green, red, etc., but my data comes up with a continuous blue scale which makes it difficult to see the different 'groups'; pca_whales<-read.table("test.txt",…
Charlotte
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Sweep warnings when using ggbiplot to plot FactoMineR's PCA object

I'm trying to adapt ggbiplot to work with the PCA data object produced by the FactoMineR package but I'm getting warnings I don't understand. Here's what I've done so far, I've added the bit starting at else if(inherits(pcobj, 'PCA')) and ending at…
Ben
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Error when installing ggbiplot r-package developer version from github

I encounter an error when installing an r-package (ggbiplot) from github. > library(devtools) > install_github("ggbiplot", "vqv") Installing ggbiplot from vqv Installing ggbiplot * checking for file…
Joc
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