Scores outside the ellipse when ellipse=TRUE

Analysis
1

Hi,
I am using DIABLO to integrate data from paired samples. When I plot the two blocks separately, the scores do not fall within the ellipses (which I understand represent confidence intervals). See image:
image

However, when I use block=“average” on the same model, all of the scores fall within the ellipses. Is this normal or have I done something wrong?

Also, it is not possible to change the axis labels once you use block=“average”. For example, X.label=“component 1” has no effect on the resulting figure until you remove block=“average”. Thank you very much for your time! Best,

erinc

2

Is this normal or have I done something wrong?

There is nothing about this which suggests something has gone wrong. It just means when using all the samples, the confidence ellipsis compensates for the wider variety of samples and extends it radii.

For example, X.label=“component 1” has no effect on the resulting figure until you remove block=“average”.

This must be a bit of a bug. I’ll have a look into this. Thanks for the heads up!

3

Hi @erinc ,

I’ve implemented a fix for the bug you pointed out. If you are really needing this feature, follow these steps to install this updated version of the package:

  1. Navigate to the R directory on your computer. Ensure the folder is titled like “R-X.X.X” (in my case, R-4.2.1). This can be found using the following command in RStudio:
> file.path(R.home())
[1] "D:/Programs/Work Programs/R-4.2.1"

  1. Go into this folder, then to library and look for mixOmics. Select the mixOmics folder and delete it.

  2. Load the devtools package (ensure you have it installed):

install.packages("devtools")
library(devtools)
  1. Download the package on the " " branch or via the specific pull request:
install_github("mixOmicsTeam/mixOmics",
               ref = github_pull("245"))
               
# OR

install_github("mixOmicsTeam/mixOmics", 
               branch = "issue-243")
  1. Load the mixOmics library, and voilà!
library(mixOmics)