## ----style, echo=FALSE, results='asis'---------------------------------------- BiocStyle::markdown() ## ----setup, echo=FALSE, message=FALSE----------------------------------------- library(Cardinal) setCardinalBPPARAM(SerialParam()) setCardinalVerbose(FALSE) RNGkind("Mersenne-Twister") ## ----eda-data, fig.height=3, fig.width=3, fig.align='center'------------------ set.seed(2020) mse <- simulateImage(preset=2, npeaks=10, dim=c(20,20), sdnoise=0.5, peakheight=c(2,4), representation="centroid") design <- makeFactor(circle=mse$circle, square=mse$square, bg=!(mse$circle | mse$square)) image(mse, design ~ x * y, key=TRUE) ## ----eda-image, fig.height=2, fig.width=7------------------------------------- image(mse, feature=c(1,4,7), layout=c(1,3)) ## ----pca---------------------------------------------------------------------- pca <- PCA(mse, ncomp=3) summary(pca) ## ----pca-image, fig.height=2, fig.width=7------------------------------------- image(pca, values="scores", superpose=FALSE, layout=c(1,3)) ## ----pca-loadings, fig.height=2, fig.width=7---------------------------------- plot(pca, values="loadings", superpose=FALSE, layout=c(1,3), lwd=2) ## ----pca-scores, fig.height=2.5, fig.width=4, fig.align='center'-------------- pca_scores <- DataFrame(resultData(pca, 1, "scores")) plot(pca_scores, PC1 ~ PC2, groups=design, pch=20) ## ----colocalized-------------------------------------------------------------- coloc <- colocalized(mse, mz=1023) coloc ## ----colocalized-images, fig.height=2, fig.width=7---------------------------- image(mse, mz=coloc$mz[1:3], layout=c(1,3)) ## ----ssc-clustering----------------------------------------------------------- ssc <- spatialShrunkenCentroids(mse, r=1, k=5, s=c(0,3,6,9)) summary(ssc) ## ----ssc-image, fig.height=3, fig.width=3------------------------------------- image(ssc, model=list(s=9), values="probability") ## ----ssc-statistic, fig.height=2.5, fig.width=4, fig.align='center'----------- plot(ssc, model=list(s=9), values="statistic", lwd=2) ## ----ssc-top------------------------------------------------------------------ ssc_top <- topFeatures(ssc, model=list(s=9), class == 1) ssc_top ## ----dgmm--------------------------------------------------------------------- dgmm <- spatialDGMM(mse, r=1, k=5, method="adaptive") summary(dgmm) ## ----dgmm-image, fig.height=2, fig.width=7------------------------------------ image(dgmm, model=list(feature=c(1,4,7)), layout=c(1,3)) ## ----dgmm-plot, fig.height=2, fig.width=7------------------------------------- plot(dgmm, model=list(feature=c(1,4,7)), layout=c(1,3)) ## ----dgmm-colocalized--------------------------------------------------------- coloc2 <- colocalized(dgmm, mse$square) subset(coloc2, select=c(-r, -k, -group)) ## ----classification-data, fig.height=2, fig.width=7--------------------------- set.seed(2020) mse2 <- simulateImage(preset=7, npeaks=10, dim=c(10,10), sdnoise=0.5, nruns=3, peakdiff=2, representation="centroid") class <- makeFactor(A=mse2$circleA, B=mse2$circleB) image(mse2, class ~ x * y, key=TRUE, layout=c(1,3)) ## ----classification-images, fig.height=2, fig.width=7------------------------- image(mse2, feature=1, layout=c(1,3)) ## ----pls-cv------------------------------------------------------------------- cv_pls <- crossValidate(mse2, .y=class, .fun=PLS, ncomp=1:5, .fold=run(mse2)) summary(cv_pls) ## ----pls---------------------------------------------------------------------- pls <- PLS(mse2, y=class, ncomp=3) summary(pls) ## ----pls-image, fig.height=2, fig.width=7------------------------------------- image(pls, values="fitted", layout=c(1,3)) ## ----pls-coefficients, fig.height=2.5, fig.width=4, fig.align='center'-------- plot(pls, values="coefficients", lwd=2) ## ----pls-scores, fig.height=2.5, fig.width=4, fig.align='center'-------------- pls_scores <- DataFrame(resultData(pls, 1, "scores")) plot(pls_scores, C1 ~ C2, groups=class, pch=20) ## ----ssc-cv------------------------------------------------------------------- cv_ssc <- crossValidate(mse2, .y=class, .fun=spatialShrunkenCentroids, r=1, s=c(0,3,6,9), .fold=run(mse2)) summary(cv_ssc) ## ----ssc-classification------------------------------------------------------- ssc2 <- spatialShrunkenCentroids(mse2, y=class, r=1, s=0) summary(ssc2) ## ----ssc-image-2, fig.height=2, fig.width=7----------------------------------- image(ssc2, layout=c(1,3)) ## ----ssc-statistic-2, fig.height=2.5, fig.width=4, fig.align='center'--------- plot(ssc2, values="statistic", lwd=2) ## ----ssc-top-2---------------------------------------------------------------- topFeatures(ssc2, class=="B") %>% subset(select=c(-diff, -r, -k, -s)) ## ----test-data, fig.height=5, fig.width=7------------------------------------- set.seed(2020) mse3 <- simulateImage(preset=4, npeaks=10, dim=c(10,10), sdnoise=0.3, nruns=3, peakdiff=1, representation="centroid") trt <- makeFactor(A=mse3$circleA, B=mse3$circleB) image(mse3, trt ~ x * y, key=TRUE, layout=c(2,3)) ## ----test-image, fig.height=5, fig.width=7------------------------------------ image(mse3, feature=1, layout=c(2,3)) ## ----test-diff---------------------------------------------------------------- featureData(mse3) ## ----test-mean-test----------------------------------------------------------- mtest <- meansTest(mse3, ~ condition, groups=run(mse3)) summary(mtest) ## ----test-mean-plot, fig.height=3, fig.width=7-------------------------------- plot(mtest, layout=c(2,5), ylab="intensity") ## ----test-mean-top------------------------------------------------------------ topFeatures(mtest, p.adjust="fdr", AdjP < .05) ## ----test-segment-dgmm-------------------------------------------------------- dgmm2 <- spatialDGMM(mse3, r=1, k=5, groups=run(mse3)) ## ----test-segment-test-------------------------------------------------------- stest <- segmentationTest(dgmm2, ~ condition, classControl="Ymax") summary(stest) ## ----test-segment-plot, fig.height=3, fig.width=7----------------------------- plot(stest, layout=c(2,5), ylab="intensity") ## ----test-segment-mapping----------------------------------------------------- image(stest, model=list(feature=3), values="mapping") ## ----test-segment-top--------------------------------------------------------- topFeatures(stest, p.adjust="fdr", AdjP < .05) %>% subset(select=c(-diff, -r, -k)) ## ----session-info------------------------------------------------------------- sessionInfo()