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Volcano plot

Source: R/cyt_volc.R
cyt_volc.Rd

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 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. Additionally, there is a choice between t‑tests and Wilcoxon rank‑sum tests and adjusting p‑values for multiple comparisons.

Usage

cyt_volc(
  data,
  group_col,
  cond1 = NULL,
  cond2 = NULL,
  fold_change_thresh = 2,
  p_value_thresh = 0.05,
  top_labels = 10,
  method = c("ttest", "wilcox"),
  p_adjust_method = NULL,
  add_effect = FALSE,
  verbose = FALSE
)

Arguments

data

A data frame containing numeric variables and a grouping column.

group_col

Character. Name of the grouping column.

cond1

Character string specifying the level of group_col for the first condition to compare.

cond2

Character strings specifying the second level of group_col to compare with cond1.

fold_change_thresh

Numeric. Threshold for absolute fold change (in original scale). Default is 2.

p_value_thresh

Numeric. Threshold for the p‑value (raw or adjusted). Default is 0.05.

top_labels

Integer. Number of top points to label in each plot. Default is 10.

method

Character. Statistical test to use. "ttest" (default) uses two‑sample t‑tests; "wilcox" uses Wilcoxon rank‑sum tests.

p_adjust_method

Character or NULL. Method to adjust p‑values across variables within each comparison (e.g., "BH"). If NULL (default) no adjustment is performed. See p.adjust for details.

add_effect

Logical. If TRUE, effect sizes are computed and returned in the results (Cohen's d for t‑tests; rank‑biserial for Wilcoxon). Default is FALSE.

verbose

Logical. If TRUE, prints the data frame used for the final comparison without the label column. Default is FALSE.

Value

A list of ggplot objects (one per comparison). Each plot visualizes log2 fold change on the x‑axis and –log10 of the (adjusted) p‑value on the y‑axis. The underlying data used to construct the final plot are printed when verbose = TRUE.

Note

If cond1 and cond2 are not provided, the function automatically generates all possible pairwise combinations of groups from the specified group_col for comparisons.

Author

Xiaohua Douglas Zhang and Shubh Saraswat

Examples

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

cyt_volc(data_df, "Group", cond1 = "T2D", cond2 = "ND", fold_change_thresh = 2.0, top_labels= 15)
#> $`T2D vs ND`

#>