ERR for Score plot (PCA)

Question

I am doing PCA in R and I got the result. But when I try to plot the first two principal components I get an error:

Warning: Ignoring unknown aesthetics: fill
Error in eval(expr, envir, enclos) : object 'GROUP' not found

Here is my code:

data = read.csv("pca_scores.csv", header = T)
data = data[, c(1:3)]
ggplot(data, aes(PC1, PC2)) +
       geom_point(aes(shape = Group)) +
       geom_text(aes(label = data$X)) +
       stat_ellipse(aes(fill = Group))

I knew the problem is the “Group”. I did not mention the group in the previous code. But I really don't know how to change it

https://i.stack.imgur.com/rHgrj.png

When asking for help, you should include a simple reproducible example with sample input and desired output that can be used to test and verify possible solutions. Pictures of data are not very helpful. If you don't have a group, just use geom_point() rather than geom_point(aes(shape = Group)). — MrFlick
Are you getting both Warning and Error of is it just one thing? And yes provide a sample of that "pca_scores.csv" — Aleh

Maurits Evers Maurits Evers · Accepted Answer · 2018-02-28T22:03:55

Agree with @MrFlick, you should always provide sample data; a screenshot of your data.frame is not useful.

That aside, you can try this:

require(tidyverse);
data %>%
    mutate(Group = gsub("\\(.+\\)$", "", X)) %>%
    ggplot(aes(PC1, PC2)) +
        geom_point(aes(shape = Group)) +
        geom_text(aes(label = X)) +
        stat_ellipse(aes(fill = Group))

A few comments:

You don't need to use data$ inside aes(); just refer to the relevant column directly.
I've added a Group column, which strips the "(PubChem: ...)" part from X.
Keep in mind that stat_ellipse will only draw an ellipse if there are >3 points.

ERR for Score plot (PCA)

1 Answers