Sample-vs-sample scatter plot per method (NormalyzerDE style)

Plots log2-intensity of one sample against another, one point per protein, for each normalization method. A linear fit and the adjusted R^2 are overlaid. Default comparison uses the first two columns of the SE (as NormalyzerDE does).

Usage

nm_plot_scatter(
  se,
  assay_names = NULL,
  condition_col = "Condition",
  sample1 = NULL,
  sample2 = NULL,
  ...
)

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.

sample1

Character. Name of the first sample (x-axis). Default = first column of se.

sample2

Character. Name of the second sample (y-axis). Default = second column of se.

...

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_scatter(se, sample1 = "A_1", sample2 = "A_2")