plot.prAM: plot.prAM

In stuchly/MetaMass: Tools for Mass Spectrometry data meta-analysis

Description

creates ROC curve of annotated clusters with respect to all used annoations.

Usage

plot.prAM(AM,abs=FALSE,legend.position="bottomleft")

Arguments

AM	AnnoMass object. Result of function analyze.MSfile
abs	logical; plot number of assigned proteins instead of recall
legend.position	character; see details in ?legend

Details

This function evaluates clustering performance via precision-recall curves with respect to the annotation

Examples

file1<-system.file("extdata","Data_Fig_1a.txt",package="MetaMass")
file1

##proteins identified by genename -> annotation.ID=2 (see ?AnnotationAM)
##cluster with respect metadata only (group=0)
res1<-analyze.MSfile(MSfile=file1,Metadata=c("Christoforou"),output="res1",markers=c(3:5))
par(mfrow=c(5,3),mar=c(1, 4, 2.2, 1) + 0.1)
plot.prAM(res1) #roc curve with respect to the 1st annotation.fraction (3rd column in AnnotationFile)

stuchly/MetaMass documentation built on Nov. 14, 2019, 10:58 p.m.