Chi Liu

Hi Natali, Could you please send me your data to reproduce the plot? I need to check how this happened step by step. Please both save your microtable object and...

Hi jose, Yes. You are right. All the parameters not found by cal_manova function will pass to adonis2 function. Please use `beta_Bray_16S$res_manova` to check your result. Best, Chi

Hi. Please attach your data `t1` so that I can reproduce the issue. To save it, please follow the tutorial to use save function (https://chiliubio.github.io/microeco_tutorial/notes.html#save-function) and attach the compressed object.

Hi. To save it to pdf or png, you should use 'method=circlize', as another method is dynamic vis that cannot be directly saved like we usually do.

Hi. Please refer to the paper (https://doi.org/10.1186/1471-2105-13-113). I will add more descriptions in the function `get_node_table`. Thanks for the reminder.

Hi. The Pi and Zi scores come from the function `get_node_table` and are stored in its result `res_node_table` inside the object. The function plot_taxa_roles is only used for the visualization....

Hi @patrickDsal Yes. You are correct. This is a bug. Thank you very much. I overlooked the ifelse logic in the function, leading to a cover of other option when...

I will try to find out the solution on your suggestion of ploting group centroids for ordination.

Could you please send me your microtable dataset and your script to repeat this?

Hi. Please use `cal_ordination_envsquare` function for the R2. If `t1$trans_ordination(adjust_arrow_length = TRUE)` still produces an error, please save your t1 object and send it to me to check it.