esm_manhattan_plot: Manhattan plot of feature-cluster association p-values

In metasnf: Meta Clustering with Similarity Network Fusion

Manhattan plot of feature-cluster association p-values

Description

Manhattan plot of feature-cluster association p-values

Usage

esm_manhattan_plot(
  esm,
  neg_log_pval_thresh = 5,
  threshold = NULL,
  point_size = 5,
  jitter_width = 0.1,
  jitter_height = 0.1,
  text_size = 15,
  plot_title = NULL,
  hide_x_labels = FALSE,
  bonferroni_line = FALSE
)

Arguments

esm	Extended solutions data frame storing associations between features and cluster assignments. See ?extend_solutions.
neg_log_pval_thresh	Threshold for negative log p-values.
threshold	P-value threshold to plot dashed line at.
point_size	Size of points in the plot.
jitter_width	Width of jitter.
jitter_height	Height of jitter.
text_size	Size of text in the plot.
plot_title	Title of the plot.
hide_x_labels	If TRUE, hides x-axis labels.
bonferroni_line	If TRUE, plots a dashed black line at the Bonferroni-corrected equivalent of the p-value threshold.

Value

A Manhattan plot (class "gg", "ggplot") showing the association p-values of features against each solution in the provided solutions data frame.

Examples

# full_dl <- data_list(
#     list(subc_v, "subcortical_volume", "neuroimaging", "continuous"),
#     list(income, "household_income", "demographics", "continuous"),
#     list(pubertal, "pubertal_status", "demographics", "continuous"),
#     list(anxiety, "anxiety", "behaviour", "ordinal"),
#     list(depress, "depressed", "behaviour", "ordinal"),
#     uid = "unique_id"
# )
# 
# dl <- full_dl[1:3]
# target_dl <- full_dl[4:5]
# 
# set.seed(42)
# sc <- snf_config(
#     dl = dl,
#     n_solutions = 20,
#     min_k = 20,
#     max_k = 50
# )
# 
# sol_df <- batch_snf(dl, sc)
# 
# ext_sol_df <- extend_solutions(
#     sol_df,
#     dl = dl,
#     target = target_dl,
#     min_pval = 1e-10 # p-values below 1e-10 will be thresholded to 1e-10
# )
# 
# esm_manhattan <- esm_manhattan_plot(
#     ext_sol_df[1:5, ],
#     neg_log_pval_thresh = 5,
#     threshold = 0.05,
#     point_size = 3,
#     jitter_width = 0.1,
#     jitter_height = 0.1,
#     plot_title = "Feature-Solution Associations",
#     text_size = 14,
#     bonferroni_line = TRUE
# )

metasnf documentation built on April 3, 2025, 5:40 p.m.