## ----style, echo=FALSE, results='asis'---------------------------------------- BiocStyle::markdown() ## ----setup, echo=FALSE, message=FALSE----------------------------------------- library(CardinalWorkflows) setCardinalBPPARAM(SerialParam()) setCardinalVerbose(FALSE) RNGkind("L'Ecuyer-CMRG") ## ----------------------------------------------------------------------------- library(Cardinal) ## ----load-pig206-------------------------------------------------------------- data(pig206, package="CardinalWorkflows") pig206 <- as(pig206, "MSImagingExperiment") ## ----show-pig206-------------------------------------------------------------- pig206 ## ----mz-885------------------------------------------------------------------- image(pig206, mz=885.5, plusminus=0.25) ## ----pig206-mean-------------------------------------------------------------- pig206_mean <- summarizeFeatures(pig206, "mean") ## ----plot-pig206-mean--------------------------------------------------------- plot(pig206_mean) ## ----pig206-tic--------------------------------------------------------------- pig206_tic <- summarizePixels(pig206, c(tic="sum")) ## ----plot-pig206-tic---------------------------------------------------------- image(pig206_tic) ## ----peak-ref-pig206---------------------------------------------------------- pig206_ref <- pig206_mean %>% peakPick(SNR=3) %>% peakAlign(ref="mean", tolerance=0.5, units="mz") %>% peakFilter() %>% process() ## ----peak-bin-pig206---------------------------------------------------------- pig206_peaks <- pig206 %>% normalize(method="tic") %>% peakBin(ref=mz(pig206_ref), tolerance=0.5, units="mz") %>% process() pig206_peaks ## ----mz-187------------------------------------------------------------------- image(pig206_peaks, mz=187) ## ----mz-840------------------------------------------------------------------- image(pig206_peaks, mz=840) ## ----mz-537------------------------------------------------------------------- image(pig206_peaks, mz=537) ## ----------------------------------------------------------------------------- pig206_pca <- PCA(pig206_peaks, ncomp=3) ## ----------------------------------------------------------------------------- image(pig206_pca, contrast.enhance="histogram", normalize.image="linear") ## ----------------------------------------------------------------------------- plot(pig206_pca, lwd=2) ## ----ssc---------------------------------------------------------------------- set.seed(1) pig206_ssc <- spatialShrunkenCentroids(pig206_peaks, method="adaptive", r=2, s=c(0,5,10,15,20,25), k=10) ## ----show-ssc----------------------------------------------------------------- summary(pig206_ssc) ## ----ssc-image-multi---------------------------------------------------------- image(pig206_ssc, model=list(s=c(10,15,20,25))) ## ----ssc-image-s20------------------------------------------------------------ image(pig206_ssc, model=list(s=20)) ## ----ssc-centers-------------------------------------------------------------- plot(pig206_ssc, model=list(s=20), lwd=2) ## ----ssc-centers-2------------------------------------------------------------ cols <- discrete.colors(6) setup.layout(c(3,1)) plot(pig206_ssc, model=list(s=20), column=1, col=cols[1], lwd=2, layout=NULL) plot(pig206_ssc, model=list(s=20), column=5, col=cols[5], lwd=2, layout=NULL) plot(pig206_ssc, model=list(s=20), column=6, col=cols[6], lwd=2, layout=NULL) ## ----ssc-statistic------------------------------------------------------------ plot(pig206_ssc, model=list(s=20), values="statistic", lwd=2) ## ----ssc-statistic-2---------------------------------------------------------- setup.layout(c(3,1)) plot(pig206_ssc, model=list(s=20), values="statistic", column=1, col=cols[1], lwd=2, layout=NULL) plot(pig206_ssc, model=list(s=20), values="statistic", column=5, col=cols[5], lwd=2, layout=NULL) plot(pig206_ssc, model=list(s=20), values="statistic", column=6, col=cols[6], lwd=2, layout=NULL) ## ----top-heart---------------------------------------------------------------- topFeatures(pig206_ssc, model=list(s=20), class==1) ## ----top-brain---------------------------------------------------------------- topFeatures(pig206_ssc, model=list(s=20), class==5) ## ----top-liver---------------------------------------------------------------- topFeatures(pig206_ssc, model=list(s=20), class==6) ## ----load-cardinal------------------------------------------------------------ data(cardinal, package="CardinalWorkflows") cardinal <- as(cardinal, "MSImagingExperiment") ## ----show-cardinal------------------------------------------------------------ cardinal ## ----cardinal-mean------------------------------------------------------------ cardinal_mean <- summarizeFeatures(cardinal, "mean") ## ----peak-ref-cardinal-------------------------------------------------------- cardinal_ref <- cardinal_mean %>% peakPick(SNR=3) %>% peakAlign(ref="mean", tolerance=0.5, units="mz") %>% peakFilter() %>% process() ## ----peak-bin-cardinal-------------------------------------------------------- cardinal_peaks <- cardinal %>% normalize(method="tic") %>% peakBin(ref=mz(cardinal_ref), tolerance=0.5, units="mz") %>% process() cardinal_peaks ## ----ssc-cardinal------------------------------------------------------------- set.seed(1) cardinal_ssc <- spatialShrunkenCentroids(cardinal_peaks, method="adaptive", r=2, s=c(10,20,30,40), k=10) ## ----show-ssc-cardinal-------------------------------------------------------- summary(cardinal_ssc) ## ----ssc-cardinal-multi------------------------------------------------------- image(cardinal_ssc) ## ----ssc-cardinal-image------------------------------------------------------- image(cardinal_ssc, model=list(s=40), col=c("1"=NA, "2"="gray", "3"="black", "4"="firebrick", "5"="brown", "6"="darkred", "7"="red")) ## ----top-body----------------------------------------------------------------- topFeatures(cardinal_ssc, model=list(s=40), class==7) image(cardinal, mz=207) ## ----top-text----------------------------------------------------------------- topFeatures(cardinal_ssc, model=list(s=40), class==3) image(cardinal, mz=649) ## ----session-info------------------------------------------------------------- sessionInfo()