evidencePlot: Create an evidence plot for a module

In tmod: Feature Set Enrichment Analysis for Metabolomics and Transcriptomics

Create an evidence plot for a module

Description

Create an evidence plot for a module

Usage

evidencePlot(
  l,
  m,
  mset = "all",
  rug = TRUE,
  roc = TRUE,
  filter = FALSE,
  unique = TRUE,
  add = FALSE,
  col = "black",
  col.rug = "#eeeeee",
  gene.labels = NULL,
  gene.colors = NULL,
  gene.lines = 1,
  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)
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	if TRUE, gene names are shown; alternatively, a named character vector with gene labels to be shown, or NULL (default) for no labels (option evaluated only if rug is plotted)
gene.colors	NULL (default) or a character vectors indicating the color for each gene. Either a named vector or a vector with the same order of genes as 'l'.
gene.lines	a number or a vector of numbers; line width for marking the genes on the rug (default=1). If the vector is named, the names should be gene ids.
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. By default, 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.

Several styles of the evidence plot are possible: * roc (default): a receiver-operator characteristic like curve; the area under the curve corresponds to the effect size (AUC) * roc_absolute: same as above, but the values are not scaled by the total number of genes in a module * gsea * enrichment: the curve shows relative enrichment at the given position

See Also

[tmod-package()], [hgEnrichmentPlot()]

Examples

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

tmod documentation built on March 31, 2023, 9 p.m.