Plot PCoA of tRNA rewiring scores. — plot_pcoa

Create a scatter plot of PCoA coordinates from perform_pcoa(), with points sized by the number of non-zero comparisons and colored by Euclidean rewiring magnitude. The top n_label isodecoders are labeled with ggrepel::geom_text_repel().

Usage

plot_pcoa_rewiring(
  pcoa_result,
  rewiring_scores,
  title = "PCoA of tRNA rewiring",
  n_label = 10
)

Arguments

pcoa_result: A list from perform_pcoa() with elements coordinates and variance_explained.
rewiring_scores: A tibble from calculate_rewiring_scores() with at least isodecoder, euclidean_magnitude, and n_nonzero columns.
title: Plot title. Default "PCoA of tRNA rewiring".
n_label: Number of top isodecoders to label. Default 10.

Value

A ggplot object.

Examples

# \donttest{
mat <- matrix(
  c(1.5, -0.8, 0.3, 2.1, 0.5, -1.2),
  nrow = 3,
  dimnames = list(
    c("tRNA-Ala", "tRNA-Gly", "tRNA-Ser"),
    c("20_vs_34", "34_vs_58")
  )
)
scores <- calculate_rewiring_scores(mat)
pcoa <- perform_pcoa(mat)
plot_pcoa_rewiring(pcoa, scores)

# }