CytoProfile (version 0.2.3)

cyt_volc: Volcano Plot.

Description

This function subsets the numeric columns from the input data and compares them based on a selected grouping column. It computes the fold changes (as the ratio of means) and associated p-values (using two-sample t-tests) for each numeric variable between two groups. The results are log2-transformed (for fold change) and -log10-transformed (for p-values) to generate a volcano plot.

Usage

cyt_volc(
  data,
  group_col,
  cond1 = NULL,
  cond2 = NULL,
  fold_change_thresh = 2,
  p_value_thresh = 0.05,
  top_labels = 10,
  verbose = FALSE
)

Value

A list of volcano plots (as ggplot objects) for each pairwise comparison. Additionally, the function prints the data frame used for plotting (excluding the significance column) from the final comparison.

Arguments

data

A matrix or data frame containing the data to be analyzed.

group_col

A character string specifying the column name used for comparisons (e.g., group, treatment, or stimulation).

cond1

A character string specifying the name of the first condition for comparison. Default is NULL.

cond2

A character string specifying the name of the second condition for comparison. Default is NULL.

fold_change_thresh

A numeric threshold for the fold change. Default is 2.

p_value_thresh

A numeric threshold for the p-value. Default is 0.05.

top_labels

An integer specifying the number of top variables to label on the plot. Default is 10.

verbose

A logical indicating whether to print the computed statistics to the console. Default is FALSE.

Author

Xiaohua Douglas Zhang and Shubh Saraswat

Examples

# Loading data
data_df <- ExampleData1[,-c(2:3)]

volc_plot <- cyt_volc(data_df, "Group", cond1 = "T2D", cond2 = "ND",
fold_change_thresh = 2.0, top_labels= 15)
print(volc_plot$`T2D vs ND`)