Visualize MiloR DA results

Usage

leo_milo_vis(
  milo_obj,
  da_results,
  plot = c(1, 2),
  layout = "UMAP.HARMONY",
  alpha = 0.05,
  log2fc_colours = c(low = "#070091", mid = "white", high = "#910000"),
  log2fc_limits = c(-5, 5),
  cell_type = "cell_anno",
  mix_threshold = 0.7,
  bee_order = NULL,
  bee_labs = c(x = "Cell Type", y = "Log Fold Change"),
  bee_add_box = TRUE
)

Arguments

milo_obj: A Milo object.
da_results: Output from miloR::testNhoods().
plot: Integer vector. Which plots to return: 1 for neighbourhood graph, 2 for beeswarm plot.
layout: Embedding stored in the Milo object (default "UMAP.HARMONY").
alpha: FDR cutoff (default 0.05).
log2fc_colours: Named vector with three colours for the log2FC gradient (c(low, mid, high)).
log2fc_limits: Two-element numeric vector giving colour-scale limits.
cell_type: Character. Column in the metadata used to annotate neighbourhoods (default "cell_anno").
mix_threshold: Minimum fraction of a single annotation to avoid calling the neighbourhood “Mixed”.
bee_order: Optional character vector specifying the display order of groups in the beeswarm plot.
bee_labs: Named character vector giving axis titles for the bee plot: (c(x = "Cell Type", y = "Log Fold Change")). If NULL, no axis labels are added.
bee_add_box: Logical. If TRUE, adds a boxplot to the beeswarm plot (default TRUE).

Value

1: UMAP of the DA; 2: bee plot of the DA results; 3: vertical bee plot; 4. DA results with cell type annotation (based on 'cell_type' params)