Remove taxa loading vector RDA

[16svale]

Dear David,
I'm wondering if it's possible to hide the taxa loading vectors (the grey lines) that are not relevant. For example, in the plot where I’ve chosen to display only the names of the top 4 relevant taxa, I’d like to also hide the other loading vectors. Including all of them makes the plot look too cluttered.

This is my current code:

Function to run the RDA

run_rda_and_plot_ASV <- function(phylo_micro, constraints, title_main, subtitle_text, caption_text, color_var) {
  # Run RDA
  rda_micro <- phylo_micro %>%
    #tax_agg("unique") %>%
    tax_transform("clr") %>%
    ord_calc(constraints = constraints, scale_cc = TRUE) %>%
    ps_mutate(SampleLabel = rownames(sample_data(.)))

  # Scaling 2 plot
  caption_scaling_2 <- paste(caption_text, "scaling 2") # Adjust caption for Scaling 2
  plot_scaling_2 <- ord_plot(rda_micro,
                             plot_taxa = 1:5, # plot labels for top 3 taxa (by longest line length)
                             constraint_lab_style = constraint_lab_style(size = 3),
                             tax_lab_style = tax_lab_style(size = 2.5, label.size = 0.1),
                             size = 4,
                             color = color_var,
                             shape = "variable 2") +
    scale_colour_brewer(palette = "Dark2") +
    ggtitle(title_main, subtitle = subtitle_text) +
    labs(caption = caption_scaling_2)

  print(plot_scaling_2)
}

run_rda_and_plot_ASV(
  phyloseq,
  constraints = c("Chitinase", "Lactonase"),#change accordingly to significant variables
  title_main = "title",
  subtitle_text = "clr-transformed genera: constraints in red, taxa in black",
  caption_text = "",
  color_var = "variable 1")

Thank you in advance for your work!

Best,
Valentina

[hisatakeishida]

Hello,

I am not sure if this is the best way, but adding tax_vec_style_all=vec_constraint(linewidth = 0, arrow = NULL) in ord_plot() seems to remove those "background" taxa loading vector.

[david-barnett]

Thanks for helping out Hisatake, that suggestion should work, as should colour = NA

library(microViz)
#> microViz version 0.12.7 - Copyright (C) 2021-2025 David Barnett
#> ! Website: https://david-barnett.github.io/microViz
#> ✔ Useful?  For citation details, run: `citation("microViz")`
#> ✖ Silence? `suppressPackageStartupMessages(library(microViz))`
data("dietswap", package = "microbiome")

aitchison_pca <- dietswap %>%
  tax_transform("clr", rank = "Genus") %>%
  ord_calc() 

aitchison_pca %>%
  ord_plot(
    colour = "bmi_group", plot_taxa = 1:5,
    tax_vec_style_all = vec_tax_all(colour = NA)
  ) 

^{Created on 2025-05-18 with reprex v2.1.1}