tmod (version 0.19)

evidencePlot: Create an evidence plot for a module

Description

Create an evidence plot for a module

Usage

evidencePlot(l, m, mset = "all", scaled = TRUE, filter = FALSE,
  add = FALSE, legend = "topleft")

Arguments

l

sorted list of HGNC gene identifiers

m

character vector of modules for which the plot should be created

mset

Which module set to use (see tmodUtest for details)

scaled

if TRUE, the cumulative sums will be divided by the total sum (default)

filter

if TRUE, genes not defined in the module set will be removed

add

if TRUE, the plot will be added to the existing plot

legend

position of the legend. If NULL, no legend will be drawn

Details

This function creates an evidence plot for a module, based on an ordered list of genes. The plot shows the receiving operator characteristic (ROC) curve and a rug below, which indicates the distribution of the module genes in the sorted list.

See Also

tmod-package, hgEnrichmentPlot

Examples

# artificially enriched list of genes
set.seed(123)
data(tmod)
bg <- tmod$GENES$ID
fg <- sample( c(tmod$MODULES2GENES[["LI.M127"]], bg[1:1000]))
l <- unique(c(fg, bg))
evidencePlot(l, "LI.M127")
evidencePlot(l, filter=tmod$GENES$ID, "LI.M127")