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dbRDA not plotting?

Open NataliHB opened this issue 2 years ago • 2 comments

Hi Chi,

I hope you are okay! I am trying to re-run some analyses after I updated microeco and I am struggling with the dbRDA graph (which I was able to get before), as it doesn't display the samples.

t1$cal_ordination(method = "dbRDA", use_measure = "bray") Use bray in dataset$beta_diversity for dbRDA ... The original ordination result is stored in object$res_ordination ... The R2 is stored in object$res_ordination_R2 ... The terms anova result is stored in object$res_ordination_terms ... The axis anova result is stored in object$res_ordination_axis ... t1$trans_ordination(adjust_arrow_length = TRUE) The result list is stored in object$res_ordination_trans ... Warning messages: 1: In scrs$biplot <- scores(res_ordination, choices = c(1, 2), "bp", : Coercing LHS to a list 2: In Ops.factor(ref[, 1], 2) : ‘^’ not meaningful for factors 3: In Ops.factor(ref[, 2], 2) : ‘^’ not meaningful for factors t1$plot_ordination(plot_color = "Well") Warning messages: 1: Removed 11 rows containing missing values (geom_segment). 2: Removed 11 rows containing missing values (geom_text_repel).

Screenshot 2022-08-04 at 00 52 07

This is what I get, have you encountered this issue before? Any help is hugely appreciated!

Cheers, Natali

NataliHB avatar Aug 03 '22 23:08 NataliHB

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 t1 object and compress them (https://chiliubio.github.io/microeco_tutorial/notes.html#save-function). You can paste the data here or send to me via email ([email protected]).

Chi

ChiLiubio avatar Aug 04 '22 03:08 ChiLiubio

Please note that dbRDA only finds one kind of scores: those for which you have calculated dissimilarities. Normally these are row scores that correspond to sites, but in your graph you seem to have variables. Is that dbRDA or normal RDA? In vegan you can add the missing scores (usually columns and corresponding species) with function sppscores<-, but I have no idea how to do that in microeco. Anyway, if you have dbRDA, it is expected to have just one kind of scores.

jarioksa avatar Aug 08 '22 09:08 jarioksa