tmod (version 0.30)

evidencePlot: Create an evidence plot for a module

Description

Create an evidence plot for a module

Usage

evidencePlot(l, m, mset = "all", scaled = TRUE, rug = TRUE, roc = TRUE, filter = FALSE, unique = TRUE, add = FALSE, col = "black", col.rug = "#eeeeee", gene.labels = NULL, gl.cex = 1, style = "roc", lwd = 1, lty = 1, rug.size = 0.2, legend = NULL, ...)

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)

rug

if TRUE, draw a rug-plot beneath the ROC curve

roc

if TRUE, draw a ROC curve above the rug-plot

filter

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

unique

if TRUE, duplicates will be removed

add

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

col

a character vector color to be used

col.rug

a character value specifying the color of the rug

gene.labels

a named character vector with gene labels to be shown (only if rug is plotted)

gl.cex

Text cex (magnification) for gene labels

style

"roc" for receiver-operator characteristic curve (default), and "gsea" for GSEA-style (Kaplan-Meier like plot)

lwd

line width (see par())

lty

line type (see par())

rug.size

fraction of the plot that should show the rug. If rug.size is 0, rug is not drawn. If rug.size is 1, ROC curve is not drawn.

legend

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

...

Further parameters passed to the plotting function

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=TRUE, "LI.M127")