library(survival) filecanc=c('breast','digothr','malegen','femgen','other','respir','colrect','lymyleuk','urinary') rb=c("red","orange","yellow","green","blue","violet") # code 5 year age groups by light spectrum for (k in 3:3) {load(paste("/SEER/",filecanc[k],".RData",sep="")) # this loads in DF if (k==1) { canc=c('Breast'); code=list(c(1741,1748)) } if (k==2) {canc=c('esophogeal','stomach','liver','pancreatic'); code=list(c(1504,1505),c(1510,1519),c(1550,1550),c(1570,1579)) } if (k==3) {canc=c("Prostate"); code=list(c(185,185))} if (k==4) {canc=c("Cervical","Uterine","Vaginal"); code=list(c(1809,1809),c(1820,1820),c(1830,1830))} if (k==5) {canc=c("Thyroid","Brain"); code=list(c(193,193),c(1911,1919))} if (k==6){canc=c("Laryngeal","Lung");code=list(c(1610,1610),c(1622,1629))} if (k==7){canc=c("Colorectal"); code=list(c(1530,1539)) } if (k==8) { canc=c("NHL", "Hodgkins", "MML" ,"ALL"," CLL", "AML", "CML") code=list(c(2000,2008),c(2015,2016),c(2030,2030),c(2040,2040),c(2041,2041),c(2050,2050),c(2051,2051))} if (k==9) { canc=c("Bladder","Kidney"); code=list(c(1880,1889),c(1890,1891))} for (i in 1:length(code)) { Indx=((DF$ICD9>=code[[i]][1])&(DF$ICD9<=code[[i]][2]))&(DF$surv!=1287)&(DF$numPrim==1) # 99*12+99 =1287 => survival time not known ageCuts=c(0,6,12,18) ageCutsY=c(0,30,60,90) par(mfcol=c(2,3)) for (j in 1:3) { ndat=DF[Indx&(DF$ageRC<=ageCuts[j+1])&(DF$ageRC>ageCuts[j]),] ndat=transform(ndat,dwd=((COD>=20010)&(COD<=37000)) ) # http://seer.cancer.gov/codrecode/1969+_d09172004/index.html # these CODs cover all cancers since numPrim=1 => same cancer is COD, if ((k!=1)&(k!=3)&(k!=4)) # plot both sexes {#print(cph <- coxph(Surv(surv,dwd)~ageRC+sex,data = ndat)) #(S=survdiff(Surv(surv,dwd)~ageRC+sex,data = ndat)) plot(survfit(Surv(surv,dwd)~ageRC,data = ndat[ndat$sex==1,]),xlim=c(0,60),xlab="Months",ylab="Survival", col=rb, main = paste(canc[i],"in males ages",ageCutsY[j],"to",ageCutsY[j+1])) plot(survfit(Surv(surv,dwd)~ageRC,data = ndat[ndat$sex==2,]),xlim=c(0,60),xlab="Months",ylab="Survival", col=rb, main = paste(canc[i],"in females ages",ageCutsY[j],"to",ageCutsY[j+1])) } if ((k==1)|(k==4)) # plot females { plot(survfit(Surv(surv,dwd)~ageRC,data = ndat[ndat$sex==2,]),xlim=c(0,ifelse(k==1,120,60)),xlab="Months",ylab="Survival", col=rb, main = paste(canc[i],"in females ages",ageCutsY[j],"to",ageCutsY[j+1])) plot.new()} # empty plot if (k==3) # plot males { plot(survfit(Surv(surv,dwd)~ageRC,data = ndat[ndat$sex==1,]),xlim=c(0,120),xlab="Months",ylab="Survival", col=rb, main = paste(canc[i],"in males ages",ageCutsY[j],"to",ageCutsY[j+1])) plot.new()} # empty plot } # j loop on age groups #locator(n=1) # point and click in figure to move ahead to next plot set dev.copy(pdf,file=paste(canc[i],".pdf",sep=""),width=8,height=6);dev.off() } # the i for loop over within file cancer types } # k loop cancer files