sig_box: Title: sig_box - Generate a Box plot with Statistical...

In IOBR/IOBR: Immune Oncology Biological Research

Title: sig_box - Generate a Box plot with Statistical Comparisons

Description

The sig_box function is designed to generate a boxplot with optional statistical comparisons. It takes in various parameters such as data, signature, variable, and more to customize the plot. It can be used to visualize and analyze data in a Seurat object or any other data frame.

Usage

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

Arguments

data	The input data, which can be a Seurat object or a data frame.
signature	The column name representing the y-axis values in the plot.
variable	The column name representing the x-axis values in the plot.
angle_x_text	The angle (in degrees) at which x-axis text labels should be displayed (default = 0).
hjust	The horizontal justification of x-axis text labels (default = 0.5).
palette	The color palette to use for filling the boxplots (default = "nrc").
cols	Optional vector of colors to use for filling the boxplots (default = NULL).
jitter	Boolean flag indicating whether to add jitter to the data points (default = FALSE).
point_size	The size of the data points when jitter is enabled (default = 5).
size_of_font	The font size for axis labels and text (default = 10).
size_of_pvalue	The font size for the statistical comparison results (default = 6).
show_pvalue	Boolean flag indicating whether to display the statistical comparison results (default = TRUE).
return_stat_res	Boolean flag indicating whether to return the statistical comparison results (default = FALSE).
assay	The name of the assay to extract data from in a Seurat object (default = NULL, uses the default assay).
slot	The slot name to extract data from in a Seurat object (default = "scale.data").
scale	Boolean flag indicating whether to scale the signature values (default = FALSE).

Author(s)

Dongqiang Zeng

Examples

data("tcga_stad_pdata", package = "IOBR")

sig_box(data = tcga_stad_pdata, signature = "TMEscore_plus", variable = "subtype", jitter = T, palette = "jco")

sig_box(data = tcga_stad_pdata, signature = "TMEscore_plus", variable = "subtype", jitter = FALSE, palette = "jco")

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