Proportion Test Plot

Generate proportion test plots based on the results from RunProportionTest.

Usage

ProportionTestPlot(
  srt,
  comparison = NULL,
  FDR_threshold = 0.05,
  log2FD_threshold = log2(1.5),
  order_by = c("value", "name"),
  pt.size = 1,
  pt.alpha = 1,
  cols.sig = "red",
  cols.ns = "grey",
  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
)

Arguments

srt: A Seurat object containing proportion test results.
comparison: A character string specifying which comparison to plot. If NULL, plots all comparisons.
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).
pt.size: The size of the points. Default is 1.
pt.alpha: The transparency of the data points. Default is 1.
cols.sig: Color for significant points and confidence intervals.
cols.ns: Color for non-significant points and confidence intervals.
aspect.ratio: Aspect ratio of the panel.
xlab: A character string specifying the x-axis label. Default is "Cell Type".
ylab: A character string specifying the y-axis label. Default is "log2 (FD)".
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". Default is "bottom".
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.

Examples

data(pancreas_sub)
pancreas_sub <- RunProportionTest(
  pancreas_sub,
  group.by = "CellType",
  split.by = "Phase"
)
#> ℹ [2026-01-27 07:52:32] Start proportion test
#> ℹ [2026-01-27 07:52:32] Running comparison: "G1" vs "S"
#> ℹ [2026-01-27 07:52:39] Running comparison: "S" vs "G1"
#> ℹ [2026-01-27 07:52:47] Running comparison: "G1" vs "G2M"
#> ℹ [2026-01-27 07:52:54] Running comparison: "G2M" vs "G1"
#> ℹ [2026-01-27 07:53:01] Running comparison: "S" vs "G1"
#> ℹ [2026-01-27 07:53:08] Running comparison: "G1" vs "S"
#> ℹ [2026-01-27 07:53:15] Running comparison: "S" vs "G2M"
#> ℹ [2026-01-27 07:53:21] Running comparison: "G2M" vs "S"
#> ℹ [2026-01-27 07:53:27] Running comparison: "G2M" vs "G1"
#> ℹ [2026-01-27 07:53:34] Running comparison: "G1" vs "G2M"
#> ℹ [2026-01-27 07:53:41] Running comparison: "G2M" vs "S"
#> ℹ [2026-01-27 07:53:48] Running comparison: "S" vs "G2M"
#> ✔ [2026-01-27 07:53:54] Proportion test completed

ProportionTestPlot(pancreas_sub)
#> Warning: Removed 1 row containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 1 row containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 2 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 2 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 1 row containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 1 row containing missing values or values outside the scale range
#> (`geom_segment()`).


# Plot specific comparisons
ProportionTestPlot(
  pancreas_sub,
  comparison = c("G2M_vs_G1", "G2M_vs_S")
)
#> Warning: Removed 2 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 1 row containing missing values or values outside the scale range
#> (`geom_segment()`).


# Plot paired comparisons using list format
ProportionTestPlot(
  pancreas_sub,
  comparison = list(c("G2M", "G1"))
)
#> Warning: Removed 2 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 2 rows containing missing values or values outside the scale range
#> (`geom_segment()`).


ProportionTestPlot(
  pancreas_sub,
  cols.sig = "blue",
  comparison = list(c("G2M", "G1"))
)
#> Warning: Removed 2 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 2 rows containing missing values or values outside the scale range
#> (`geom_segment()`).

Usage

Arguments

See also

Examples