Proportion Test Plot

Generate differential abundance visualizations from outputs of RunProportionTest. Main display styles are effect-size view and UMAP projection view, while legacy plot types remain callable for compatibility.

Usage

ProportionTestPlot(
  srt,
  comparison = NULL,
  proportion_method = NULL,
  result_level = c("group", "neighborhood"),
  plot_type = c(
    "effect",
    "umap",
    "volcano",
    "manhattan",
    "ring",
    "milo_beeswarm",
    "milo_graph",
    "sccoda_forest"
  ),
  umap_mode = c("discrete", "continuous"),
  reduction = "UMAP",
  projection_args = list(),
  FDR_threshold = 0.05,
  log2FD_threshold = log2(1.5),
  order_by = c("value", "name"),
  palette = "RdBu",
  palcolor = NULL,
  group_palette = "Chinese",
  group_palcolor = NULL,
  pt.size = 1,
  pt.alpha = 1,
  cols.sig = "red",
  cols.ns = "grey",
  cols.increase = "#d7301f",
  cols.decrease = "#2b8cbe",
  effect_color_mode = c("directional", "classic"),
  nlabel = 5,
  features_label = NULL,
  label = FALSE,
  label.fg = "black",
  label.bg = "white",
  label.bg.r = 0.1,
  label.size = 4,
  aspect.ratio = NULL,
  xlab = "Cell Type",
  ylab = "log2 (FD)",
  theme_use = "theme_scop",
  theme_args = list(),
  legend.position = "bottom",
  legend.direction = "vertical",
  legend.title = "Significance",
  combine = TRUE,
  nrow = NULL,
  ncol = NULL,
  byrow = TRUE,
  seed = 11
)

Arguments

srt: A Seurat object containing proportion test results.
comparison: A character vector specifying which comparisons to plot. If NULL, all stored comparisons are plotted.
proportion_method: Optional method to select from method-layer results. If NULL, active/most recent method is used.
result_level: Result level for plotting: "group" or "neighborhood".
plot_type: Plot type. Main recommended values are "effect" and "umap". Legacy values are retained for compatibility: "volcano", "manhattan", "ring", "milo_beeswarm", "milo_graph", and "sccoda_forest".
umap_mode: UMAP mapping mode when plot_type = "umap". "discrete" maps cells to Increased/Decreased/NS; "continuous" maps group-level obs_log2FD.
reduction: Reduction name used for UMAP projection.
projection_args: Additional arguments passed through to CellDimPlot (discrete mode) or FeatureDimPlot (continuous mode).
FDR_threshold: FDR value cutoff for significance.
log2FD_threshold: Absolute value of log2FD cutoff for significance.
order_by: Method to order clusters. Options: "name", "value".
palette: Palette name for continuous effect coloring.
palcolor: Custom colors for palette.
group_palette: Palette name for cluster/group coloring.
group_palcolor: Custom colors for group_palette.
pt.size: Point size.
pt.alpha: Point transparency.
cols.sig: Legacy color for significant/credible points and intervals.
cols.ns: Color for non-significant points and intervals.
cols.increase: Color for increased DA groups in directional effect mode.
cols.decrease: Color for decreased DA groups in directional effect mode.
effect_color_mode: Effect color style: "directional" (default) or "classic".
nlabel: Number of labels when label = TRUE and features_label = NULL.
features_label: Character vector specifying labels to draw.
label: Whether to draw labels.
label.fg: Label foreground color.
label.bg: Label background color.
label.bg.r: Label background rounding radius.
label.size: Label size.
aspect.ratio: Aspect ratio of each panel.
xlab: X-axis label.
ylab: Y-axis label.
theme_use: Theme used. Can be a character string or a theme function.
theme_args: Additional arguments passed to theme_use.
legend.position: Legend position.
legend.direction: Legend direction.
legend.title: Legend title.
combine: Whether to combine into one patchwork object.
nrow: Number of rows for combined plot.
ncol: Number of columns for combined plot.
byrow: Arrange panels by row.
seed: Random seed used for jitter and label ranking ties.

Usage

Arguments

See also