bioarch/classify_example.R at master · franticspider/bioarch · GitHub

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#/* Copyright (C) 2014 Simon Hickinbotham, Matthew Collins, Keri Roswell  */
#/* When you use this, send an email to: simon.hickinbotham@york.ac.uk    */
#/* with an appropriate reference to your work.                           */

#/* This file is part of exportBruker version 1.0.2  		  	  */

#/* exportBruker is free software: you can redistribute it and/or modify  */
#/* it under the terms of the GNU General Public License as published by  */
#/* the Free Software Foundation, either version 3 of the License, or     */
#/* (at your option) any later version.                                   */

#/* This program is distributed in the hope that it will be useful,       */
#/* but WITHOUT ANY WARRANTY; without even the implied warranty of        */
#/* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the         */
#/* GNU General Public License for more details.                          */

#/* You should have received a copy of the GNU General Public License     */
#/* along with this program.  If not, see <http://www.gnu.org/licenses/>. */


library("MALDIquantForeign")
library("bioarch")
#source("exportBruker.R")
#source("flamePlot_3.R")


getclass <- function(idx,fn){
	name = "unknown"
	t <- read.table(fn,sep='\t')
	#'b' %in% v
	if(idx %in% t[,1]){
		name<-t[grep(idx,t[,1]),3]
		message(sprintf("found a %s entry at %s",name,idx))
	}
	return(name)

}


moff = -1
mrange = 4

message("Loading known average sheep, goat and cow data")
#fallowG9<- import('../FallowDeer/Fallow deer_0_G9.txt')
#fallowH9<- import('../FallowDeer/Fallow deer_0_H9.txt')
#fallowI9<- import('../FallowDeer/Fallow deer_0_I9.txt')

if(!exists("sheep"))
sheep <- import("/home/sjh/Desktop/sjh/bioarch/SF/SFData/averaged/Averaged Sheep Spectrum.txt")
if(!exists("goat"))
goat <- import("/home/sjh/Desktop/sjh/bioarch/SF/SFData/averaged/Averaged Goat Spectrum.txt")
if(!exists("cow"))
cow <- import("/home/sjh/Desktop/sjh/bioarch/SF/SFData/averaged/Averaged Cow Spectrum.txt")


message("Loading ref vals for sheep, goat and cow")
massTable<-read.table('/home/sjh/Desktop/sjh/bioarch/SF/SFData/refmasses.tsv')

sheepTable<-massTable[grep("Sheep",massTable[,1]),]
sheepVals<-as.integer(sheepTable[,3:ncol(sheepTable)])
sheepLB<-sheepVals+moff
sheepUB<-sheepVals+mrange


goatTable<-massTable[grep("Goat",massTable[,1]),]
goatVals<-as.integer(goatTable[,3:ncol(goatTable)])
goatLB<-goatVals+moff
goatUB<-goatVals+mrange


cowTable<-massTable[grep("Cattle",massTable[,1]),]
cowVals<-as.integer(cowTable[,3:ncol(cowTable)])
cowLB<-cowVals+moff
cowUB<-cowVals+mrange


message("Creating combined data values")

LB = sort(unique(c(sheepLB,goatLB,cowLB)))
UB = sort(unique(c(sheepUB,goatUB,cowUB)))
lbl = list(sheepLB,goatLB,cowLB)
ubl = list(sheepUB,goatUB,cowUB)


if(!exists("testdata"))
testdata <- bioarch_loadBrukerXML("/home/sjh/Desktop/sjh/bioarch/SF/SFData/20140307_SF_UPenn164-181/")

t1 <- testdata[[1]]
t1l <- list(t1)

refdata <- list(sheep,goat,cow)

fn = sprintf("/home/sjh/plotclass.pdf",t1l[[1]]@metaData$name)

pdf(file=fn,width = 14,height=8)

for(ii in 1:length(testdata)){


	t1<-testdata[[ii]]
	t1l<-list(t1)


	#get the platemap location index
	iname <- substr(t1l[[1]]@metaData$fullName,nchar(t1l[[1]]@metaData$sampleName)+2,nchar(testdata[[1]]@metaData$sampleName)+4)
	inum <-strtoi(substr(iname,2,3), base = 0L)
	in2 <- sprintf("%s%02d",substr(iname,1,1),inum)
	message(sprintf("iname = %s, inum = %d, in2 = %s",iname,inum,in2))

	class <- getclass(in2,"/home/sjh/Desktop/sjh/bioarch/SF/SFData/platemap_classes.txt")
	message(sprintf("Outside of getclass, name for %s is %s",in2,class))


	ffn = sprintf("%s",t1l[[1]]@metaData$name)
	message(sprintf("%02d: Processing %s...",ii,ffn))

	fn = sprintf("Classification of %s (%s)",t1l[[1]]@metaData$name,class)


	classnames=c("Sheep","Goat","Cattle")

	plotclass_v2(fn,onepdf=T,refdata,t1l,0,uselag=TRUE,LB,UB,lbl,ubl,classnames)


	#plotclass_v2bits(fn,onepdf=T,refdata,t1l,0,uselag=TRUE,LB,UB,lbl,ubl,classnames)


	#fn = sprintf("pdf/%s_vs_cowD8.pdf",t1l[[1]]@metaData$name)
	#message(sprintf("testing for cow, using D8, output in %s",fn))
	#plotcomp(fn,cowD8,t1l,50,uselag=TRUE,cowLB,cowUB)

	#fn = sprintf("pdf/%s_vs_cowD7.pdf",t1l[[1]]@metaData$name)
	#message(sprintf("testing for cow, using D8, output in %s",fn))
	#plotcomp(fn,cowD7,t1l,50,uselag=TRUE,cowLB,cowUB)

}
dev.off()


#spots <- c("C4","C9","C4","C8")
#plotRuminants("20131024_TedG1_A2_C9_C4_C8.pdf",data,spots)
#plotccfs("20131024_TedG1_A2_C9_C4_C8_ccf.pdf",data,spots,100)
#plotflame("20131024_TedG1_A2_C9_C4_C8_flame.pdf",data,spots,100)


#spots <- c("C4","C8")
#plotcomp("20131024_TedG1_C4vsC8.pdf",fallowG9,list(testdata[[1]]),spots,150)