Replace chord diagram with tRNA structure plot in rewiring vignette

Use plot_tRNA_structure() with linkage arcs to show significant rewiring
for tRNA-Glu-TTC, replacing the chord diagram visualization.

Author: jayhesselberth

vignettes/articles/rewiring.Rmd

@@ -121,21 +121,24 @@ pcoa <- perform_pcoa(mat)
 plot_pcoa_rewiring(pcoa, scores)
 ```
 
-## Network visualization
+## Structure visualization
 
-Build a chord diagram from the ROR data to visualize modification rewiring
-between positions.
+Plot significant rewiring linkages on the tRNA cloverleaf structure for a
+single isodecoder.
 
 ```{r}
-#| label: fig-chord-ror
-#| fig.cap: "Chord diagram of modification rewiring between control and infected conditions."
-#| fig.width: 6
-#| fig.height: 6
-ror_agg <- ror |>
-  dplyr::group_by(pos1, pos2) |>
-  dplyr::summarise(log_ror = mean(ror), .groups = "drop")
-
-plot_chord_ror(ror_agg, title = "Modification rewiring: inf vs ctl")
+#| label: fig-structure-ror
+#| fig.cap: "tRNA structure showing significant modification rewiring linkages for tRNA-Glu-TTC."
+ror_glu <- ror |>
+  filter(isodecoder == "tRNA-Glu-TTC", significant) |>
+  rename(value = ror)
+
+svg <- plot_tRNA_structure(
+  "tRNA-Glu-TTC",
+  "Escherichia coli",
+  linkages = ror_glu
+)
+structure_html(svg)
 ```
 
 ## Session info