Plot a differential-expression MA plot

Plot a differential-expression MA plot

Usage

plot_de_ma(
  result,
  coef = NULL,
  fdr = 0.05,
  min_abs_effect = 1,
  label_features = NULL,
  feature_labels = NULL,
  abundance = NULL,
  abundance_column = NULL,
  abundance_transform = c("auto", "identity", "log10")
)

Arguments

result

Input accepted by de_table().

coef

Optional coefficient passed to de_table().

fdr

Maximum adjusted p-value.

min_abs_effect

Minimum absolute effect estimate.

label_features

Feature identifiers to label; no features are selected for labels automatically.

feature_labels

Optional complete feature-named labels or a named feature-label column in a data frame result.

abundance

Optional complete feature-named abundance vector.

abundance_column

Optional abundance column in a data-frame result.

abundance_transform

Display abundance unchanged, on a base-10 log axis, or choose the backend convention automatically. Zero abundances are omitted from a log10 plot; negative abundances are rejected.

Value

An unprinted standard ggplot object carrying recommended physical dimensions for plot_save().

See also

Other plotting: plot_assay_heatmap(), plot_de_volcano(), plot_embedding(), plot_gsea_classic(), plot_gsea_ridge(), plot_ora_bubble(), plot_ora_network(), plot_ora_radial(), plot_qc_correlation(), plot_qc_library(), plot_qc_outliers(), plot_save(), theme_bulkmae()