4 Visualizing raw TIMA results

This vignette describes additional helper functions to visualize TIMA results.

Visualization

To check the full results:

plots <- cascade::prepare_tima_annotations(
  show_example = TRUE
) |> 
  cascade::plot_tima()
# cascade::prepare_tima_annotations(
#   annotations = list(
#     "yourExperiment1"="PathToYourTimaOutput1",
#     "yourExperiment2"="PathToYourTimaOutput2"
#     )
# ) |> 
#   cascade::plot_tima()

plots$histogram

plots$treemap

plots$sunburst

To compare annotated and predicted classes:

list(
  cascade::prepare_tima_annotations(
    show_example = TRUE
    ),
  cascade::prepare_tima_annotations(
    show_example = TRUE,
    predicted_classes = TRUE
    )
  ) |>
  tidytable::bind_rows() |>
  list() |>
  cascade::plot_tima() |>
  purrr::pluck("histogram")

To compare different filtering thresholds:

list(
  cascade::prepare_tima_annotations(
    show_example = TRUE
  ), 
  cascade::prepare_tima_annotations(
    show_example = TRUE,
    min_score_biological = 0.2,
    min_score_final = 0.4
  ),
  cascade::prepare_tima_annotations(
    show_example = TRUE,
    min_score_initial = 0.2,
    min_score_biological = 0.2,
    min_score_chemical = 0.2,
    min_score_final = 0.4,
    min_matched_peaks_absolute = 6L,
    min_matched_peaks_percentage = 0.5,
    min_peaks = 10L
    )
  ) |>
  tidytable::bind_rows() |>
  list() |> 
  cascade::plot_tima() |>
  purrr::pluck("histogram")

We hope you enjoyed using CASCADE and are pleased to hear from you!

For any remark or suggestion, please fill an issue or feel free to contact us directly.

Adriano Rutz

2025-05-19

Visualization