sig_box_batch: Batch Signature Box Plots for Group Comparisons

In IOBR: Immune Oncology Biological Research

Batch Signature Box Plots for Group Comparisons

Description

Generates multiple box plots for specified features (signatures) across groups in the input data. Supports customization of plot appearance, output path, statistical annotation, and compatibility with Seurat objects. Plots are saved to the specified directory or a default folder.

Usage

sig_box_batch(
  input,
  vars,
  groups,
  pattern_vars = FALSE,
  path = NULL,
  index = 0,
  angle_x_text = 0,
  hjust = 0.5,
  palette = "jama",
  cols = NULL,
  jitter = FALSE,
  point_size = 5,
  size_of_font = 8,
  size_of_pvalue = 4.5,
  show_pvalue = TRUE,
  return_stat_res = FALSE,
  assay = NULL,
  slot = "scale.data",
  scale = FALSE,
  height = 5,
  width = 3.5,
  fig_type = "pdf",
  max_count_feas = 30
)

Arguments

input	Data frame or Seurat object containing the data for analysis.
vars	Character vector. Features or variables to analyze. When 'pattern_vars = TRUE', these are treated as regular expression patterns.
groups	Character vector. Grouping variable(s) for comparison.
pattern_vars	Logical indicating whether to treat 'vars' as regular expression patterns for matching column names. Default is 'FALSE'.
path	Character string or 'NULL'. Directory to save plots. If 'NULL', plots are not saved. Default is 'NULL'.
index	Integer. Starting index for plot filenames. Default is '0'.
angle_x_text	Numeric. Angle of x-axis labels in degrees. Default is '0'.
hjust	Numeric. Horizontal justification of x-axis labels. Default is '0.5'.
palette	Character. Color palette for plots. Default is '"jama"'.
cols	Character vector or 'NULL'. Custom colors for plot elements.
jitter	Logical indicating whether to add jittered points. Default is 'FALSE'.
point_size	Numeric. Size of points. Default is '5'.
size_of_font	Numeric. Base font size. Default is '8'.
size_of_pvalue	Numeric. Size of p-value text. Default is '4.5'.
show_pvalue	Logical indicating whether to display p-values. Default is 'TRUE'.
return_stat_res	Logical indicating whether to return statistical results instead of saving plots. Default is 'FALSE'.
assay	Character string or 'NULL'. Assay type for Seurat objects.
slot	Character. Data slot for Seurat objects. Default is '"scale.data"'.
scale	Logical indicating whether to scale data before analysis. Default is 'FALSE'.
height	Numeric. Height of plots in inches. Default is '5'.
width	Numeric. Width of plots in inches. Default is '3.5'.
fig_type	Character. File format for plots (e.g., '"pdf"', '"png"'). Default is '"pdf"'.
max_count_feas	Integer. Maximum number of features to analyze when 'pattern_vars = TRUE'. If matched variables exceed this limit, only the first 'max_count_feas' features are used. Default is '30'.

Value

If 'return_stat_res = TRUE', returns a data frame of statistical results; otherwise, invisibly returns the path to saved plots.

Author(s)

Dongqiang Zeng

Examples

# Simulate data
set.seed(123)
sim_pdata <- data.frame(
  ID = paste0("Sample", 1:50),
  subtype = sample(c("TypeA", "TypeB", "TypeC"), 50, replace = TRUE),
  TMEscore_plus = rnorm(50),
  GZMB = rnorm(50)
)
sig_box_batch(
  input = sim_pdata,
  vars = c("TMEscore_plus", "GZMB"),
  groups = "subtype",
  jitter = TRUE,
  palette = "jco",
  path = tempdir()
)

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