plotIndiv with ind.names=T not working

Analysis
1

Hi,
I am running the following code:

pca.result_scaled <- pca(data, scale=T)
plotIndiv(pca.result_scaled, ind.names = TRUE, pch=NULL)

As you can see, I. have three extreme outliers which I would like to exclude before proceeding to PLS-DA analysis but I am not able to identify which samples these are. I get dots instead of the ind.names despite

`

ind.names = TRUE, pch=NULL

`
testing with pch=F just gives me squares. I am using the latest dev version 6.17.28
Can you please help me identify these samples?
Thank you very much!
/Stef

Screenshot 2021-08-16 at 09.31.22
Screenshot 2021-08-16 at 09.31.22706×445 20.4 KB

2

Hi, I would very. much appreciate some input so that I can move on with. my analysis :slight_smile:
Thank you so much!
/Stef

3

hi @stepra
can you check that you have the latest version, and also that you actually do have rownames in your data?

By default the code should show the row names:

data(multidrug)
X <- multidrug$ABC.trans
pca.res <- pca(X, ncomp = 4, scale = TRUE)
plotIndiv(pca.res)

Other option (see ?pca) is to use the ind.names option but you need to specify the individual names (or any character vector associated to your individuals).
plotIndiv(pca.res, ind.names = multidrug$cell.line$Class)

Kim-Anh

4

I am also using the MixOmix 6.17.28 and having the same issue where the ind.names does not display only circles.

I tried the second line in your example and there was no change to the IndivPlot still circles no ind.names
Please help. should i revert back to mixOmics6.16.3 had other issues with that but the indv.names displayed