coef_plot_from_owas {epiomics}

Create volcano plot using results from owas

Description

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

Usage

coef_plot_from_owas(
  df,
  main_cat_var = NULL,
  order_effects = TRUE,
  highlight_adj_p = TRUE,
  highlight_adj_p_threshold = 0.05,
  effect_ratio = FALSE,
  flip_axis = FALSE,
  filter_p_less_than = 1
)

Arguments

df

output from owas function call, using conf_int = TRUE.

main_cat_var

Which variable should be the primary categorical variable? Should be either var_name or feature_name. Only relevant if both var_name and feature_name have more than one level. Default is NULL, and the y-axis is chosen as the variable that has more levels.

order_effects

Should features be ordered by the mean effect estimate? Default is TRUE.

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.

effect_ratio

Are the effect estimates on the ratio scale (ie, should the null effect line be centered at 1)? Defaults to FALSE.

flip_axis

Flip the x and y axis? Default is FALSE, and the y-axis is plotted with the features or variable names.

filter_p_less_than

P-value threshold for which features/variables will be included in the plot. Default is 1, and all features will be included.

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", 
                 conf_int = TRUE)

coef_plot_from_owas(owas_out)