volcano_owas {epiomics}

Create volcano plot using results from owas

Description

Creates a volcano plot based on ggplot using the results from the owas function.

Usage

volcano_owas(
  df,
  annotate_ftrs = TRUE,
  annotation_p_threshold = 0.05,
  highlight_adj_p = TRUE,
  highlight_adj_p_threshold = 0.05,
  horizontal_line_p_value = 0.05
)

Arguments

df

output from owas function call

annotate_ftrs

Should features be annotated with the feature name? Default is TRUE. If necessary can change the p_value_threshold as well.

annotation_p_threshold

If annotate_ftrs = TRUE, can set annotation_p_threshold to change the p-value threshold for which features will be annotated. Defaults to 0.05.

highlight_adj_p

Should features which meet a specific adjusted p-value threshold be highlighted? Default is TRUE.

highlight_adj_p_threshold

If highlight_adj_p = TRUE, can set annotation_adj_p_threshold to change the adjusted p-value threshold for which features will be highlighted. Defaults to 0.05.

horizontal_line_p_value

Set the p-value for the horizontal line for the threshold of significance.

Value

A ggplot figure

Examples

data("example_data")

# Get names of omics
colnames_omic_fts <- colnames(example_data)[
  grep("feature_",
       colnames(example_data))][1:5]

# Run function with continuous exposure as the variable of interest
owas_out <- owas(df = example_data,
                 var = "exposure1",
                 omics = colnames_omic_fts,
                 covars = c("age", "sex"),
                 var_exposure_or_outcome = "exposure",
                 family = "gaussian")

vp <- volcano_owas(owas_out)