sig_box_batch: Title sig_box_batch

In IOBR/IOBR: Immune Oncology Biological Research

Title sig_box_batch

Description

The sig_box_batch function is used to generate multiple signature box plots for analyzing the relationship between variables and groups in a given input data. It takes the input data, a vector of features or variables to analyze, and a vector of groups or categories to group the analysis by. The function allows customization of various parameters such as the path to save the figures, the appearance of the plots, and the statistical details to include. The generated figures are saved in the specified path 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	The input data for analysis.
vars	A vector of features or variables to analyze.
groups	A vector of groups or categories to group the analysis by.
pattern_vars	A logical value indicating whether the feature names specified in 'vars' should be treated as patterns to match. If set to TRUE, the function will search for matching column names in the input data and use them for analysis.
path	The path to save the generated figures. If not specified, a default folder named "1-sig-box-batch" will be created.
index	The index number to start naming the generated figures.
angle_x_text	The angle of the x-axis labels in the figures.
hjust	The horizontal alignment of the x-axis labels in the figures.
palette	The color palette to use for the figures.
cols	A vector of colors to use for the elements in the figures.
jitter	A logical value indicating whether to add jitter to the points in the figures.
point_size	The size of the points in the figures.
size_of_font	The size of the font in the figures.
size_of_pvalue	The size of the p-value text in the figures.
show_pvalue	A logical value indicating whether to show the p-value in the figures.
return_stat_res	A logical value indicating whether to return the statistical results.
assay	The assay or data type to use for analysis (for Seurat object)
slot	The slot in the data to use for analysis. (for Seurat object)
scale	A logical value indicating whether to scale the data before analysis.
height	The height of the generated figures.
width	The width of the generated figures.
fig_type	The file format to save the generated figures (e.g., "pdf").

Author(s)

Dongqiang Zeng

Examples

data("tcga_stad_pdata", package = "IOBR")
sig_box_batch(data = tcga_stad_pdata, vars = c("TMEscore_plus", "GZMB"), groups = "subtype", jitter = T, palette = "jco")

IOBR/IOBR documentation built on May 5, 2024, 2:34 p.m.