Proportion Test Plot

Generate differential-abundance plots based on results from RunProportionTest. Supports both legacy storage and method-layer storage from the multi-method proportion-test workflow.

Usage

ProportionTestPlot(
  srt,
  comparison = NULL,
  proportion_method = NULL,
  result_level = c("group"),
  plot_type = c("effect", "umap"),
  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,
  verbose = TRUE
)

Arguments

srt: A Seurat object containing proportion-test results.
comparison: A character string specifying which comparison to plot. If NULL, plots all comparisons.
proportion_method: Optional method to select from srt@tools[['ProportionTest']][['methods']]. If NULL, uses the active/most recent method.
result_level: Result level to draw. Currently only "group" is used.
plot_type: Plot type. One of "effect" or "umap".
umap_mode: UMAP projection mode for plot_type = "umap". "discrete" maps cells to DA direction categories; "continuous" maps cells to group-level obs_log2FD.
reduction: Reduction name used by UMAP projection.
projection_args: Additional arguments passed to CellDimPlot (umap_mode = "discrete") or FeatureDimPlot (umap_mode = "continuous").
FDR_threshold: FDR value cutoff for significance.
log2FD_threshold: Absolute value of log2FD cutoff for significance.
order_by: Method to order clusters. Options: "name" (alphabetical), "value" (by log2FD value).
palette: Color palette name for continuous effect coloring.
palcolor: Custom colors for palette.
group_palette: Palette for cluster/group coloring.
group_palcolor: Custom colors for group_palette.
pt.size: The size of the points.
pt.alpha: Point transparency.
cols.sig: Color for significant/credible points and intervals.
cols.ns: Color for non-significant points and intervals.
cols.increase: Default color for increased DA groups.
cols.decrease: Default color for decreased DA groups.
effect_color_mode: Coloring mode for plot_type = "effect". Use "directional" (default) for increased/decreased/NS colors, or "classic" for legacy significant/non-significant coloring.
nlabel: Number of labels added when label = TRUE and features_label = NULL.
features_label: Character vector specifying points to label.
label: Whether to add labels.
label.fg: Label foreground color.
label.bg: Label background color.
label.bg.r: Label background radius.
label.size: Label text size.
aspect.ratio: Aspect ratio of the panel.
xlab: A character string specifying the x-axis label. For plot_type = "umap", this is forwarded to the projection plot when set.
ylab: A character string specifying the y-axis label. For plot_type = "umap", this is forwarded to the projection plot when set.
theme_use: Theme used. Can be a character string or a theme function. Default is "theme_scop".
theme_args: Other arguments passed to the theme_use. Default is list().
legend.position: The position of legends, one of "none", "left", "right", "bottom", "top".
legend.direction: The direction of the legend in the plot. Can be one of "vertical" or "horizontal".
legend.title: Title of the legend.
combine: Combine plots into a single patchwork object. If FALSE, return a list of ggplot objects.
nrow: Number of rows in the combined plot. Default is NULL, which means determined automatically based on the number of plots.
ncol: Number of columns in the combined plot. Default is NULL, which means determined automatically based on the number of plots.
byrow: Whether to arrange the plots by row in the combined plot. Default is TRUE.
seed: Random seed for reproducibility. Default is 11.
verbose: Whether to print the message. Default is TRUE.

Examples

data(pancreas_sub)
pancreas_sub <- standard_scop(pancreas_sub)
pancreas_sub <- RunProportionTest(
  pancreas_sub,
  group.by = "CellType",
  split.by = "Phase",
  proportion_method = "permutation"
)

ProportionTestPlot(pancreas_sub)

ProportionTestPlot(
  pancreas_sub,
  reduction = "UMAP",
  plot_type = "umap",
  xlab = "UMAP_1",
  ylab = "UMAP_2"
)

Usage

Arguments

See also

Examples