Dot plot of top pathways for a single latent variable

Lollipop-style dot plot showing the top pathways associated with one selected LV. Dot size encodes AUC; dot colour encodes -log10(FDR). The x-axis and pathway ordering can use either AUC or -log10(FDR).

Usage

CLAMPdotplot(
  clampRes,
  lv = 1,
  top = 20,
  auc.cutoff = 0.6,
  fdr.cutoff = 0.05,
  max.name.len = 50,
  x.axis = c("AUC", "-log10(FDR)", "log10FDR"),
  order.by = x.axis
)

Arguments

clampRes

A CLAMP result list containing a summary data frame, or the summary data frame itself.

lv

LV to plot: either a numeric index (e.g. 1 -> "LV1") or a character name (e.g. "LV3"). Default 1.

top

Maximum number of pathways to display, chosen by order.by. Default 20.

auc.cutoff

Minimum AUC to display. Default 0.6.

fdr.cutoff

Maximum FDR to display. Default 0.05.

max.name.len

Maximum characters for pathway label trimming. Default 50.

x.axis

Metric to place on the x-axis. Use "AUC" or "-log10(FDR)". "log10FDR" is also accepted. Default "AUC".

order.by

Metric used to choose the top pathways and order the y-axis. Use "AUC" or "-log10(FDR)". "log10FDR" is also accepted. Defaults to x.axis.

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, 0.05),
    stringsAsFactors = FALSE
)

CLAMPdotplot(list(summary = summ), lv = 1, top = 10)

CLAMPdotplot(list(summary = summ),
    lv = "LV2", x.axis = "-log10(FDR)",
    order.by = "-log10(FDR)"
)