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Signature Box Plot with Statistical Comparisons

Source: R/sig_box.R
sig_box.Rd

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

Dongqiang Zeng

Examples

tcga_stad_pdata <- load_data("tcga_stad_pdata")
sig_box(
  data = tcga_stad_pdata,
  signature = "TMEscore_plus",
  variable = "subtype",
  jitter = TRUE,
  palette = "jco"
)
#> Warning: The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
#> ℹ Please use the `linewidth` argument instead.
#> ℹ The deprecated feature was likely used in the IOBR package.
#>   Please report the issue at <https://github.com/IOBR/IOBR/issues>.