can't hide ellipseline

[little2b]

I have set ellipseLineSize = 0,but there is still ellipseline in my picture.

[kevinblighe]

Can you please show the code that you are running.

[little2b]

this is my code:

biplot(p,
       x='PC1',
       y = 'PC2',
       labSize = 0.25,
       pointSize = 1,
       colby = 'group',colkey = c('Tumor'='forestgreen','Normal'='red'),
        ellipse = TRUE,
        ellipseType = 't',
        ellipseLevel = 0.95,
        ellipseFill = TRUE,
        ellipseAlpha = 1/4,
        ellipseLineSize = 0,
        ellipseFillKey = c('Tumor'='yellow','Normal'='pink'),
       legendPosition = 'top')

[kevinblighe]

Thank you. Have you gone through the vignette to see if it works from there?

[little2b]

yes it like this but i want ellipse line is hidden, and i set a code:ellipseLineSize = 0 but it is still exist

[kevinblighe]

No, please run the vignette code. The function works there. Please see the second plot from here: https://github.com/kevinblighe/PCAtools#stat-ellipses

[little2b]

I coped your code for the second plot and ran it:

biplot(p,
       colby = 'group', colkey = c('Tumor'='forestgreen','Normal'='purple'),
       # ellipse config
       ellipse = TRUE,
       ellipseType = 't',
       ellipseLevel = 0.95,
       ellipseFill = TRUE,
       ellipseAlpha = 1/4,
       ellipseLineSize = 0,
       ellipseFillKey = c('Tumor' = 'yellow', 'Normal' = 'pink'),
       xlim = c(-125,125), ylim = c(-50, 80),
       hline = 0, vline = c(-25, 0, 25),
       legendPosition = 'top', legendLabSize = 16, legendIconSize = 8.0)

but the line is still here

[kevinblighe]

That is not quite what I meant. Please run the vignette code, from start to finish, and let me know if that works.

[little2b]

I'm very sorry for causing you trouble, but what is the vignette code.

[kevinblighe]

Ah, my apologies! It just means can you run the code, starting from here: https://github.com/kevinblighe/PCAtools#2-load-the-package-into-r-session

Then, when you get to the part with ellipseLineSize, how does it work?