CytoProfile (version 0.2.3)

cyt_errbp: Error-bar Plot.

Description

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.

Usage

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

Value

An error-bar plot (a ggplot object) is produced and optionally saved as a PDF. If output_file is specified, the function returns returns the ggplot object.

Arguments

data

A data frame containing the data for each group. It should include at least one numeric column for the measurements and a column specifying the group membership.

group_col

Character. The name of the column in data that specifies the group membership.

p_lab

Logical. If TRUE, p-values are displayed on the plot. Default is FALSE.

es_lab

Logical. If TRUE, effect sizes (SSMD) are displayed on the plot. Default is FALSE.

class_symbol

Logical. If TRUE, significance and effect size are represented using symbolic notation (e.g., *, **, >, <<). If FALSE, numeric values are used. Default is TRUE.

x_lab

Character. Label for the x-axis. If not provided, defaults to the name of the group_col or "Group" if group_col is NULL.

y_lab

Character. Label for the y-axis. If not provided, defaults to "Value".

title

Character. Title of the plot. If not provided, a default title is generated based on the measured variables.

log2

Logical. If TRUE, a log2 transformation (with a +1 offset) is applied to all numeric columns before analysis. Default is FALSE.

output_file

Character. The file path to save the plot as a PDF. If NULL, the plot is displayed but not saved. Default is NULL.

Author

Xiaohua Douglas Zhang and Shubh Saraswat

Details

The function performs the following steps:

1. Optionally applies a log2 transformation to numeric data.

2. Determines the baseline group (the first level of group_col).

3. Calculates summary statistics (sample size, mean, standard deviation) for each group and each numeric variable.

4. Performs t-tests to compare each group against the baseline for each numeric variable.

5. Computes effect sizes (SSMD) for each group compared to the baseline.

6. Generates a faceted error-bar plot, with one facet per numeric variable.

7. Optionally adds p-value and effect size labels to the plot.

8. Optionally saves the plot as a PDF.

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)