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Proportion Test Plot

Source: R/ProportionTestPlot.R
ProportionTestPlot.Rd

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(
  object,
  comparison = NULL,
  proportion_method = NULL,
  result_level = c("group", "neighborhood"),
  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,
  srt = NULL
)

Arguments

object

A Seurat object containing proportion-test results.

comparison

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. Use "group" for group-level results or "neighborhood" for stored Milo neighborhood-level results. A missing requested level is an error. Milo group results are sample-level cell-type proportion tests, distinct from the Milo neighborhood test.

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 group-level obs_log2FD or the mean effect of overlapping Milo neighborhoods to cells. Neighborhood directions are based on significant memberships: opposite directions are "Mixed", while cells in no neighborhood are "Uncovered". This is a member-cell projection, not a separate Milo test per cell.

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 frequentist methods. Milo neighborhood results use SpatialFDR. scCODA uses its stored credible decision instead.

log2FD_threshold

Absolute value of log2FD cutoff for frequentist methods; not applied to scCODA credibility.

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

X-axis label. For plot_type = "umap", this is forwarded to the projection plot when set.

ylab

Y-axis label. For plot_type = "umap", this is forwarded to the projection plot when set.

theme_use, theme_args

Theme name or function, plus extra theme arguments.

legend.position

The position of legends, one of "none", "left", "right", "bottom", "top".

legend.direction

Legend direction: "horizontal" or "vertical".

legend.title

Title of the legend.

combine, nrow, ncol, byrow

Combine plots with patchwork::patchwork. combine = FALSE returns a list of ggplots.

seed

Random seed.

verbose

Whether to print messages.

srt

Deprecated alias for object; supply exactly one of the two. It will be removed in scop 1.0.0.

See also

RunProportionTest

Examples

data(pancreas_sub)
pancreas_sub <- RunStandardWorkflow(pancreas_sub)
#> ℹ [2026-10-11 23:02:51] Start standard processing workflow...
#> ℹ [2026-10-11 23:02:51] Checking a list of <Seurat>...
#> ! [2026-10-11 23:02:51] Data 1/1 of the `srt_list` is "unknown"
#> ℹ [2026-10-11 23:02:51] Perform `NormalizeData()` with `normalization.method = 'LogNormalize'` on 1/1 of `srt_list`...
#> ℹ [2026-10-11 23:02:51] Perform `FindVariableFeatures()` on 1/1 of `srt_list`...
#> ℹ [2026-10-11 23:02:51] Use the separate HVF from `srt_list`
#> ℹ [2026-10-11 23:02:51] Number of available HVF: 2000
#> ℹ [2026-10-11 23:02:51] Finished check
#> ℹ [2026-10-11 23:02:51] Perform `ScaleData()`
#> ℹ [2026-10-11 23:02:51] Perform pca linear dimension reduction
#> ℹ [2026-10-11 23:02:52] Use stored estimated dimensions 1:23 for Standardpca
#> ℹ [2026-10-11 23:02:52] Perform `Seurat::FindClusters()` with `cluster_algorithm = 'louvain'` and `cluster_resolution = 0.6`
#> ℹ [2026-10-11 23:02:52] Reorder clusters...
#> ℹ [2026-10-11 23:02:52] Skip `log1p()` because `layer = data` is not "counts"
#> ℹ [2026-10-11 23:02:52] Perform umap nonlinear dimension reduction
#> ✔ [2026-10-11 23:02:58] Standard processing workflow completed
pancreas_sub <- RunProportionTest(
  pancreas_sub,
  group.by = "CellType",
  split.by = "Phase",
  proportion_method = "permutation"
)
#> ℹ [2026-10-11 23:02:58] Start proportion test ("permutation")
#> ℹ [2026-10-11 23:02:58] Running comparison: "G1" vs "S"
#> ℹ [2026-10-11 23:02:59] Running comparison: "G1" vs "G2M"
#> ℹ [2026-10-11 23:03:02] Running comparison: "S" vs "G2M"
#> ℹ [2026-10-11 23:03:02] Running comparison: "S" vs "G1"
#> ℹ [2026-10-11 23:03:02] Running comparison: "G2M" vs "G1"
#> ℹ [2026-10-11 23:03:02] Running comparison: "G2M" vs "S"
#> ✔ [2026-10-11 23:03:02] Proportion test completed ("permutation")

ProportionTestPlot(pancreas_sub)


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