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Bar chart of group-separation metrics per normalization method

Source: R/Normalization_Metrics.R
nm_plot_metrics.Rd

Calls nm_compute_metrics() internally and produces a faceted bar chart (one facet per metric, free y-scales) with labeled values.

Usage

nm_plot_metrics(
  se,
  assay_names = NULL,
  condition_col = "Condition",
  seed = 42L,
  ...
)

Arguments

se

SummarizedExperiment from import_norm_matrices().

assay_names

Character vector of assay names to include. NULL = all.

condition_col

Column in colData with condition labels.

seed

Integer. Seed for the two metrics that use randomness: the Hopkins statistic, which samples random reference points, and the PERMANOVA p-value, which permutes the group labels. Without it neither column is reproducible between runs. The caller's RNG state is restored on exit. Default 42.

...

Additional arguments (unused).

Value

ggplot object.

Examples

data(nadia_dia)
se <- nm_prepare_se(nadia_dia, verbose = FALSE)
se <- nm_run_normalizations(se, methods = c("cycloess", "quantile", "MAD"),
                            verbose = FALSE)

nm_plot_metrics(se)