Error-bar Plot — cyt_errbp • CytokineProfileShinyApp

This function generates an error-bar plot to visually compare different groups against a designated baseline group. It displays the central tendency (mean or median) as a bar and overlays error bars to represent the data's spread (e.g., standard deviation, MAD, or standard error). The plot can also include p-value and effect size labels (based on SSMD), presented either as symbols or numeric values, to highlight significant differences and the magnitude of effects. When an output filename is provided the plot is saved to disk; otherwise the ggplot object is returned and drawn on the current graphics device.

Usage

cyt_errbp(
  data,
  group_col = NULL,
  p_lab = TRUE,
  es_lab = TRUE,
  class_symbol = FALSE,
  x_lab = "",
  y_lab = "",
  title = "",
  stat = c("mean", "median"),
  error = c("se", "sd", "mad", "ci"),
  scale = c("none", "log2", "log10", "zscore", "custom"),
  custom_fn = NULL,
  method = c("auto", "ttest", "wilcox"),
  p_adjust_method = NULL,
  label_size = 4,
  n_col = NULL,
  base_size = 11,
  fill_palette = NULL,
  font_settings = NULL,
  output_file = NULL,
  progress = NULL
)

Arguments

data: A data frame containing at least one numeric column and a grouping column.
group_col: Character string naming the column that defines groups. This column will be coerced to a factor.
p_lab: Logical. If TRUE (default) p-value labels are displayed for group comparisons.
es_lab: Logical. If TRUE (default) effect-size labels are displayed.
class_symbol: Logical. If TRUE, p-value and effect-size labels are encoded using symbols (e.g., *, >>>). If FALSE (default), numeric values are shown instead.
x_lab: Character string for the x-axis label. If empty a default label is generated.
y_lab: Character string for the y-axis label. If empty a default label is generated.
title: Character string for the plot title. If empty a default title is generated.
stat: Character. Central tendency statistic to use. One of "mean" (default) or "median".
error: Character. Error measure visualized around the statistic. One of "se" (standard error; default), "sd" (standard deviation), "mad" (median absolute deviation), or "ci" (approximate 95% confidence interval).
scale: Character controlling data transformation before analysis. One of "none" (default), "log2", "log10", "zscore", or "custom".
custom_fn: A user-supplied function applied to numeric columns when scale = "custom".
method: Character controlling the statistical test used for pairwise comparisons. One of "auto" (default; choose between t-test and Wilcoxon based on a normality test), "ttest", or "wilcox".
p_adjust_method: Character. If non-NULL, specifies the method passed to p.adjust() to correct p-values across all comparisons (e.g., "BH" for Benjamini-Hochberg). NULL (default) skips adjustment.
label_size: Numeric. Font size for p-value and effect-size labels. Default is 4.
n_col: Integer. Number of columns in the facet grid. If NULL (default), uses min(3, number_of_cytokines).
base_size: Numeric. Base font size for the plot theme. Default is 11.
fill_palette: Character vector of colors for the group bars. If NULL (default), all bars are filled with "gray80". Supply one color per group level (e.g. c("#4E79A7", "#F28E2B", "#E15759")).
font_settings: Optional named list of font sizes for supported plot text elements.
output_file: Optional file path. If provided, the plot is saved using ggsave(); otherwise the plot is returned and automatically printed.
progress: Optional. A Shiny Progress object for reporting progress updates.

Value

A ggplot object. When output_file is specified the plot is saved to disk and returned invisibly.

Author

Xiaohua Douglas Zhang and Shubh Saraswat

Examples

data(ExampleData1)
df <- ExampleData1[, c("Group", "CCL.20.MIP.3A", "IL.10")]
cyt_errbp(df, group_col = "Group")

cyt_errbp(df, group_col = "Group", stat = "mean", error = "sd",
          scale = "log2", class_symbol = TRUE, method = "ttest")