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Questions tagged [biplot]

46 questions
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Adding ind labels to a pca biplot

I'm making a biplot for a PCA, but the individuals are only showing up as points. Is there any way to keep the variables and individuals grouped and have the name label appear over each point? I ask this because it's important to see the groups they…
David RV
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Using theme() from ggplot2 with the factoextra package to change aesthics of biplot made

I made a successful biplot using the factoextra package (fviz_pca_biplot()), but I want to change the size of the axis labels and titles as well as changing the color of the axis lines using ggtheme theme(). I used this code and nothing changes…
Kayla
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Observation number as marker in PCA using Plotly in R

Below is the base code for visualizing a Principal Components Analysis (PCA) using Plotly in R. It is taken from the Plotly website. library(plotly) library(stats) data(iris) X <- subset(iris, select = -c(Species)) prin_comp <- prcomp(X, rank. =…
via1408
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Incorrect number of dimensions in metaMDS and scores (biplot, NMDS ordination) in R

I am trying to make a biplot in R using the vegan package: shared_tbl <-read_tsv("data/andok.shared") my data is like this…
vicey
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Cannot get the color to work in a biplot from the RDA procedure in Vegan

I have run RDA from Vegan, and cannot generate four different colors in the "sites" on the plot that correspond to the Group trait which really is countries. The problem is colvec[Group] that fails to link up the four colors with the four different…
Larry Leamy
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How to remove border line of the circles at fviz_pca_biplot in R?

I have one data below df<-structure(list(SEASON = c("Low D", "Low D", "Low D", "Low D", "Low D", "Low D", "Low D", "Low D", "Low D", "Low D", "High D", "High D", "High D", "High D", "High D", "High D", "High D", "High D", "High D", "High D"),…
Jin.w.Kim
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PCA Biplot Make Readable

I am working with California Housing Dataset. The dataset has 20640 observations and 10 attributes. I am using R to make biplot but the figure I obtained is not very readable. The output is as followenter image description here I am using a simple…
user13601395
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unable to change labels in PCA prcomp from row numbers to site names

I have followed the answers in https://stackoverflow.com/questions/38900698/how-to-change-labels-from-pca-using-prcomp-to-sample-names but am unable to get it to work. I have set up a dummy file (called tf4) with 7 columns and 12 rows and imported…
Rachel
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R CCA - Can species scores be related to CCA axis & how does the biplot arrow length relates to significance of variables?

Hallo this is my first question in stackoverflow or any simliar forum, so please excuse and be kind if I missed something out ;) I am using the vegan package in R to calculate a cca analysis. Because my study is about intraspecific variation of…
Marlon Schwienbacher
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how to generate a plot with 2 o more legend using 2 data frame in R

I'm trying to make a function using ggplot2 with 2 data frames. The fist data frame: head(DF1, 15) # with 280 rows SeqTech S1 S2 C1 C2 AM.AD.1 Sanger -1.0436581 -0.37756924 -0.7685488 -0.0441722 AM.AD.2…
abraham
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Add circles to group individuals with a second factor on a Biplot using fviz_pca

thanks for reading me. Im new with R so im lost on: how can i add group circles defined by a second factor on a biplot made with fviz_pca? I have this Table and want to apply a PCA to obtain a biplot where individuals are classified (colored) by the…
Cristóbal Jaraba Nilo
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Interpretation of PCA biplot

I need to understand what the scatterplot created by 2 principal components convey. I was working on the 'boston housing' dataset from the 'sklearn.datasets' library. I standardized the predictors and the used 'PCA' from 'sklearn.decomposition'…
ABHIRAJ SURESH
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I want to create a subset of my dataframe by how subjects cluster in the biplot

This is one of the biplots that I am working on. Circles represent clusters that I want to create a subset dataframe from If I'm interested in the top cluster, how do I select data that lies within the rectangle -.1 < PC1 <.1 & .8 < PC2 < 1.6? I…
Will Chance
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How can I reverse the axis in a biplot

When I plot a PCA and then the corresponding biplot, the axis are not always in the same direction, just like in these pictures: These are the functions, I used: (pc <- prcomp(dat5, center=T, retx=T, scale=T)); summary(pc) plot(pc$x[,1:2],…
Nicole Origami Fox
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How can I adjust the dimension of the axes fviz_pca

I'm trying to put the two axes of my biplot exactly equally scaled (i.e., 1 cm on the vertical axis must represent the same 1 cm on the horizontal axis). How can I do that with fviz_pca? or there is some better pca package? My…
Maba
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