Open cpanse opened 4 years ago
code snippet by Dierk-Christoph Pöther
#Package handling library(rawDiag) library(ggplot2) library(dplyr) library(viridisLite) #read .raw-file raw<-read.raw(file.path("path","xy.raw")) #BasePeak/TIC&InjectionTime rawMS<-raw[raw$MSOrder=="Ms",] ggplot(data=rawMS)+ geom_line(aes(rawMS$StartTime,rawMS$BasePeakIntensity))+ #rawMS$TIC instead of BasePeakIntensity geom_jitter(aes(rawMS$StartTime,rawMS$IonInjectionTimems*5*10^6),size=0.1,col="red",alpha=0.2)+ scale_y_continuous(sec.axis=sec_axis(~./(5*10^6))) #BasePeak/TIC&CycleTime CT<-calc.cycle.time(x = raw) rawCT<-merge(x=raw[,c("StartTime","BasePeakIntensity","TIC")],y=CT[,c("StartTime","CycleTime")],by.x="StartTime",all.x=T) ggplot(data=rawCT)+ geom_line(aes(rawCT$StartTime,rawCT$BasePeakIntensity))+ #rawMS$TIC instead of BasePeakIntensity geom_jitter(aes(rawCT$StartTime,rawCT$CycleTime*1*10^9),size=0.1,col="red",alpha=0.2)+ scale_y_continuous(sec.axis=sec_axis(~./(1*10^9))) #BasePeak/TIC&CycleLoad MSN<-na.omit(raw%>%dplyr::count(MasterScanNumber)) cycload<-merge(x=raw[,c("MasterScanNumber","StartTime","BasePeakIntensity","TIC")],y=MSN[,c("MasterScanNumber","n")],by.x="MasterScanNumber",all.x=T) ggplot(data=cycload)+ geom_line(aes(cycload$StartTime,cycload$BasePeakIntensity))+ #rawMS$TIC instead of BasePeakIntensity geom_jitter(aes(cycload$StartTime,cycload$n*1*10^8),size=0.1,col="red",alpha=0.2,height=0.1*10^8)+ scale_y_continuous(sec.axis=sec_axis(~./(1*10^8))) ##BasePeak/TIC&precursor/RT rawMS2<-raw[raw$MSOrder=="Ms2",] MS2<-merge(x=raw[,c("StartTime","BasePeakIntensity","TIC")],y=rawMS2[,c("StartTime","PrecursorMass")],by.x="StartTime",all.x=T) ggplot(data=MS2)+ geom_line(aes(MS2$StartTime,MS2$BasePeakIntensity))+ #rawMS$TIC instead of BasePeakIntensity geom_hex(aes(MS2$StartTime,MS2$PrecursorMass*5*10^5),bins=50)+scale_fill_viridis_c(alpha=0.7)+ scale_y_continuous(sec.axis=sec_axis(~./(5*10^5))) pdf("C:/Users/Dierk/Desktop/overlays.pdf",paper="a4r",width=297/2.54,height=210/2.54) print(Fig11) print(Fig12) print(Fig13) print(Fig14) dev.off()
code snippet by Dierk-Christoph Pöther