plotROC: Plot ROC curves

In wrProteo: Proteomics Data Analysis Functions

Plot ROC curves

Description

plotROC plots ROC curves based on results from summarizeForROC. This function plots only, it does not return any data. It allows printing simultaneously multiple ROC curves from different studies, it is also compatible with data from 3 species mix as in proteomics benchmark. Input can be prepared using moderTest2grp followed by summarizeForROC.

Usage

plotROC(
  dat,
  ...,
  useColumn = 2:3,
  methNames = NULL,
  col = NULL,
  pch = 1,
  bg = NULL,
  tit = NULL,
  xlim = NULL,
  ylim = NULL,
  point05 = 0.05,
  pointSi = 0.85,
  nByMeth = NULL,
  speciesOrder = NULL,
  txtLoc = NULL,
  legCex = 0.72,
  las = 1,
  addSuplT = TRUE,
  silent = FALSE,
  debug = FALSE,
  callFrom = NULL
)

Arguments

dat	(matrix) from testing (eg summarizeForROC )
...	optional additional data-sets to include as seprate ROC-curves to same plot (must be of same type of format as 'dat')
useColumn	(integer or character, length=2) columns from dat to be used for pecificity and sensitivity
methNames	(character) names of methods (data-sets) to be displayed
col	(character) custom colors for lines and text (choose one color for each different data-set)
pch	(integer) type of symbol to be used (see also par)
bg	(character) background color in plot (see also par)
tit	(character) custom title
xlim	(numeric, length=2) custom x-axis limits
ylim	(numeric, length=2) custom y-axis limits
point05	(numeric) specific point to highlight in plot (typically at alpha=0.05)
pointSi	(numeric) size of points (as expansion factor cex)
nByMeth	(integer) value of n to display
speciesOrder	(integer) custom order of species in legend
txtLoc	(numeric, length=3) location for text (x, y location and proportional factor for line-offset, default is c(0.4,0.3,0.04))
legCex	(numeric) cex expansion factor for legend (see also par)
las	(numeric) factor for text-orientation (see also par)
addSuplT	(logical) add text with information about precision,accuracy and FDR
silent	(logical) suppress messages
debug	(logical) display additional messages for debugging
callFrom	(character) allow easier tracking of message(s) produced

Value

This function returns only a plot with ROC curves

See Also

summarizeForROC, moderTest2grp

Examples

roc0 <- cbind(alph=c(2e-6,4e-5,4e-4,2.7e-3,1.6e-2,4.2e-2,8.3e-2,1.7e-1,2.7e-1,4.1e-1,5.3e-1,
	 6.8e-1,8.3e-1,9.7e-1), spec=c(1,1,1,1,0.957,0.915,0.915,0.809,0.702,0.489,0.362,0.234,
  0.128,0.0426), sens=c(0,0,0.145,0.942,2.54,2.68,3.33,3.99,4.71,5.87,6.67,8.04,8.77,
  9.93)/10, n.pos.a=c(0,0,0,0,2,4,4,9,14,24,36,41) )
plotROC(roc0)

wrProteo documentation built on April 12, 2025, 1:16 a.m.