sig_box: Signature Box Plot with Statistical Comparisons

In IOBR: Immune Oncology Biological Research

Signature Box Plot with Statistical Comparisons

Description

Creates box plots to visualize signature distributions across groups with optional statistical pairwise comparisons. Supports both data frames and Seurat objects for single-cell data visualization.

Usage

sig_box(
  data,
  signature,
  variable,
  palette = "nrc",
  cols = NULL,
  jitter = FALSE,
  point_size = 5,
  angle_x_text = 0,
  hjust = 0.5,
  show_pairwise_p = TRUE,
  show_overall_p = FALSE,
  return_stat_res = FALSE,
  size_of_pvalue = 6,
  size_of_font = 10,
  assay = NULL,
  slot = "scale.data",
  scale = FALSE
)

Arguments

data	Data frame or Seurat object containing the signature and grouping variable.
signature	Character string specifying the column name (or feature name in Seurat) for the signature values to plot on the y-axis.
variable	Character string specifying the grouping variable column name for the x-axis.
palette	Character string specifying the color palette name. Default is '"nrc"'.
cols	Character vector of custom fill colors. If 'NULL', palette is used. Default is 'NULL'.
jitter	Logical indicating whether to add jittered points to the box plot. Default is 'FALSE'.
point_size	Numeric value specifying the size of jittered points. Default is 5.
angle_x_text	Numeric value specifying the rotation angle for x-axis labels (in degrees). Default is 0.
hjust	Numeric value specifying the horizontal justification of x-axis labels. Default is 0.5.
show_pairwise_p	Logical indicating whether to display pairwise comparison p-values between groups. Default is 'TRUE'.
show_overall_p	Logical indicating whether to display the overall group difference p-value. Default is 'FALSE'.
return_stat_res	Logical indicating whether to return statistical test results instead of the plot. Default is 'FALSE'.
size_of_pvalue	Numeric value specifying the font size for p-values. Default is 6.
size_of_font	Numeric value specifying the base font size. Default is 10.
assay	Character string specifying the assay name (for Seurat objects). Default is 'NULL'.
slot	Character string specifying the slot name (for Seurat objects). Default is '"scale.data"'.
scale	Logical indicating whether to scale signature values (z-score transformation). Default is 'FALSE'.

Value

If 'return_stat_res = FALSE', returns a ggplot2 object. If 'return_stat_res = TRUE', returns a data frame containing statistical test results.

Author(s)

Dongqiang Zeng

Examples

# Create small example data
set.seed(123)
test_data <- data.frame(
  subtype = rep(c("A", "B"), each = 50),
  TMEscore_plus = rnorm(100)
)
sig_box(
  data = test_data,
  signature = "TMEscore_plus",
  variable = "subtype",
  jitter = TRUE,
  palette = "jco"
)

IOBR documentation built on May 30, 2026, 5:07 p.m.