| plot_aligned_trajectories | R Documentation | 
Render date-aligned trajectories for a pair of taxa and a given set of hosts. This allows us to eyeball whether taxa strongly correlated within hosts show similar dynamics across hosts.
plot_aligned_trajectories(
  output_dir,
  tax_idx1,
  tax_idx2,
  tax_label1,
  tax_label2,
  metadata,
  bind_taxa = FALSE,
  return_plot = FALSE,
  file_tag = NULL
)
| output_dir | specifies the subdirectory of the model fits directory in which to save the predictions | 
| tax_idx1 | index of first taxon | 
| tax_idx2 | index of second taxon | 
| tax_label1 | readable label for first taxon | 
| tax_label2 | readable label for second taxon | 
| metadata | metadata data.frame (with sname and collection_date column) | 
| bind_taxa | plot all trajectories for taxon 1 together; ditto taxon 2 | 
| return_plot | if TRUE, returns the ggplot2 object instead of saving it | 
| file_tag | if not NULL, a tag to append to the saved filename | 
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