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.
pt.alpha: The transparency of the points.
cols.sig: Color for significant points and confidence intervals.
cols.ns: Color for non-significant points and confidence intervals.
aspect.ratio: The aspect ratio of the plot.
xlab: A character string specifying the x-axis label.
ylab: A character string specifying the y-axis label.
theme_use: A character string specifying the theme to use for the plot.
theme_args: A list of theme arguments to pass to the theme_use function.
legend.position: Position of the legend.
legend.direction: Direction of the legend.
legend.title: Title of the legend.
combine: Whether to combine the plots for each comparison into a single plot.
nrow: An integer value specifying the number of rows in the combined plot.
ncol: An integer value specifying the number of columns in the combined plot.
byrow: Whether to arrange the plots by row in the combined plot.

Examples

data(pancreas_sub)
pancreas_sub <- RunProportionTest(
  pancreas_sub,
  group.by = "CellType",
  split.by = "Phase"
)
#> ℹ [2025-11-13 12:01:42] Start proportion test
#> ℹ [2025-11-13 12:01:42] Running comparison: "G1" vs "S"
#> ℹ [2025-11-13 12:01:49] Running comparison: "S" vs "G1"
#> ℹ [2025-11-13 12:01:56] Running comparison: "G1" vs "G2M"
#> ℹ [2025-11-13 12:02:03] Running comparison: "G2M" vs "G1"
#> ℹ [2025-11-13 12:02:09] Running comparison: "S" vs "G1"
#> ℹ [2025-11-13 12:02:16] Running comparison: "G1" vs "S"
#> ℹ [2025-11-13 12:02:23] Running comparison: "S" vs "G2M"
#> ℹ [2025-11-13 12:02:30] Running comparison: "G2M" vs "S"
#> ℹ [2025-11-13 12:02:36] Running comparison: "G2M" vs "G1"
#> ℹ [2025-11-13 12:02:43] Running comparison: "G1" vs "G2M"
#> ℹ [2025-11-13 12:02:50] Running comparison: "G2M" vs "S"
#> ℹ [2025-11-13 12:02:56] Running comparison: "S" vs "G2M"
#> ✔ [2025-11-13 12:03:02] Proportion test completed

ProportionTestPlot(pancreas_sub)


# Plot specific comparisons
ProportionTestPlot(
  pancreas_sub,
  comparison = c("G2M_vs_G1", "G2M_vs_S")
)


# Plot paired comparisons using list format
ProportionTestPlot(
  pancreas_sub,
  comparison = list(c("G2M", "G1"))
)


ProportionTestPlot(
  pancreas_sub,
  cols.sig = "blue",
  comparison = list(c("G2M", "G1"))
)

Usage

Arguments

See also

Examples