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Error Bar Plot with P-value and Effect Size Annotations

Source: R/cyt_errbp.R
cyt_errbp.Rd

This function automatically detects a numeric measurement column from the provided data and calculates group metrics (sample size, mean, standard deviation, standard error) and performs a t-test (comparing each group to the baseline) to obtain p-values and a standardized mean difference (as a proxy for effect size). When a grouping variable is provided, it is used to separate the data into groups (the first level is taken as the baseline). If no grouping variable is provided, the metrics are computed for the overall data. The function then produces a ggplot2 bar plot with error bars and, if requested, overlays p-value and effect size annotations (displayed as symbols by default).

Usage

cyt_errbp(
  data,
  group_col = NULL,
  p_lab = FALSE,
  es_lab = FALSE,
  class_symbol = TRUE,
  x_lab = "",
  y_lab = "",
  title = NULL,
  progress = NULL,
  log2 = FALSE,
  output_file = NULL
)

Arguments

data

A data frame containing at least one numeric variable. If a grouping variable is provided, it must be one of the columns.

group_col

Character. (Optional) The name of the grouping (categorical) variable. If not provided, metrics are calculated for the overall data.

p_lab

Logical. Whether to display p-value labels. Default is FALSE.

es_lab

Logical. Whether to display effect size labels. Default is FALSE.

class_symbol

Logical. If TRUE, p-values and effect sizes are shown as symbols; if FALSE, numeric values are displayed. Default is FALSE.

x_lab

Character. Label for the x-axis. Defaults to the grouping variable name if provided, or "Group" otherwise.

y_lab

Character. Label for the y-axis. Defaults to the name of the selected numeric variable.

title

Character. The plot title.

log2

Logical. If TRUE, transforms numeric variables using log2 transformation. If FALSE, uses raw values from provided data. Default is FALSE.

output_file

Optional. A string representing the file path for the PDF file to be created. If NULL (default), the function returns a list of ggplot objects.

Value

A ggplot2 object representing the error bar plot.

Examples

data <- ExampleData1

cyt_errbp(data[,c("Group", "CCL.20.MIP.3A", "IL.10")], group_col = "Group",
p_lab = TRUE, es_lab = TRUE, class_symbol = TRUE, x_lab = "Cytokines",
y_lab = "Concentrations in log2 scale", log2 = TRUE)