Plot predicted leave-one-out probabilities

Usage

volcanoPlot(
  sce,
  target,
  group,
  p_cutoff = NULL,
  fc_cutoff = 1,
  assay_type = "tfmfeatures"
)

Arguments

sce: A SingleCellExperiment object
target: Name of target variable for prediction
group: Grouping variable for cross-validation, e.g., patient
p_cutoff: Cut-off for statistical significance. A horizontal line will be drawn at -log10(p_cutoff).
fc_cutoff: Cut-off for absolute log2 fold-change. A vertical lines will be drawn at fc_cutoff.
assay_type: A string specifying the assay

Value

ggplot2 object

Examples

set.seed(23)
cell_file <- generate_data()
sce <- loadData(cell_file)
sce <- transformLogScale(sce)

sce$Drug <- as.factor(sce$Drug)
sce$Drug <- relevel(sce$Drug, ref = "D1")
types <- c("AreaShape", "Intensity", "Texture")

sce_single <- predictLOO(
    sce,
    target = "Drug", group = "Patient",
    interest_level = "D7", reference_level = "D1",
    types = types,
    n_threads = 1
)

volcanoPlot(sce_single,
    target = "Drug", group = "Patient",
    p_cutoff = 0.05, fc_cutoff = 0.5
)