Dot plot of pathway-LV associations across all latent variables

Source: R/plots.R

Produces a dot plot where each point represents one pathway × LV pair. Dot size encodes the AUC value and dot colour encodes -log10(FDR). Only associations passing auc.cutoff and fdr.cutoff are shown.

CLAMPdotplotAll(
  clampRes,
  auc.cutoff = 0.6,
  fdr.cutoff = 0.05,
  top.per.lv = NULL,
  max.name.len = 40
)

Arguments

clampRes

A CLAMP result list containing a summary data frame with columns pathway, LV, AUC, and FDR. Alternatively, clampRes may be the summary data frame itself.

auc.cutoff

Minimum AUC to display. Default 0.6.

fdr.cutoff

Maximum FDR to display. Default 0.05.

top.per.lv

Maximum number of pathways to display per LV, chosen by highest AUC. NULL shows all. Default NULL.

max.name.len

Maximum characters for pathway label trimming. Default 40.

Value

Invisibly returns a ggplot2::ggplot() object.

Examples

set.seed(9)
pathways <- paste0("Pathway_", 1:20)
lvs <- paste0("LV", 1:5)
nr <- length(pathways) * length(lvs)

summ <- data.frame(
    pathway = rep(pathways, length(lvs)),
    LV = rep(lvs, each = length(pathways)),
    AUC = runif(nr, 0.5, 1.0),
    FDR = runif(nr, 0, 0.2),
    stringsAsFactors = FALSE
)

CLAMPdotplotAll(list(summary = summ), auc.cutoff = 0.6, fdr.cutoff = 0.15)