error in volcano3D

[jaskozi]

Hi!
First, thanks for the awesome package.
I've just tested it, and replicated the vignette you explained here without any problems.
https://towardsdatascience.com/interactive-differential-expression-analysis-with-volcano3d-cf6c37b5aa6a

Then I used my data, with the disclaimer that I tested it on methylation data, and everything is working fine except the volcano3D function.

I get the following message:

Error in data.frame(x = rep(c(max(r_breaks) * cospi(0:200/100), NA), n_z_breaks),  : 
  arguments imply differing number of rows: 0, 404, 1
In addition: Warning message:
In max(z_breaks) : no non-missing arguments to max; returning -Inf

Could it be because of my data-specific values?
instead of fold change I'm using estimate which then ranges usually from 0.0 to 0.35.
and the values in the matrix range from 0.0 to 1.0.

Thank you very much!

Jasko

[KatrionaGoldmann]

Hi @EzicJ , thanks for your comment.

This looks like it is related to the cylindrical grid. I guess a problem is arising on the z-axis if the rest of your code works fine, i.e. the p-value for multi-group comparisons. Have you passed in a statistic such as ANOVA or likelihood ratio tests to show overall significance between groups, for example with anova_pvalue columns:

polar <- polar_coords(
  sampledata,
  contrast,
  pvalues,
  expression,
  multi_group_prefix = "anova"
)

What do you get for your polar@multi_group_test ?

If you try to create your own grid does this work? :

grid <- polar_grid(r_vector=polar@polar$r_zscore,
           z_vector=NULL,
           r_axis_ticks = NULL,
           z_axis_ticks = c(0, 8, 16, 32),
           n_spokes = 4)

[EzicJ]

Hi @KatrionaGoldmann,

I just re-started R to do what you said, and unexplainably now it's working :)

Thanks for your quick reply!

[KatrionaGoldmann]

Great! The trusty turn it off and on again :)