### R code from vignette source 'TTMap.Rnw' ################################################### ### code chunk number 1: style-Sweave ################################################### BiocStyle::latex() ################################################### ### code chunk number 2: loadLibAndData ################################################### library(airway) data(airway) airway <- airway[rowSums(assay(airway))>80,] assay(airway) <- log(assay(airway)+1,2) experiment <- TTMap::make_matrices(airway,seq_len(4),seq_len(4)+4, NAME = rownames(airway), CLID =rownames(airway)) ################################################### ### code chunk number 3: part1 ################################################### E=1 Pw=1.1 Bw=0 TTMAP_part1prime <-TTMap::control_adjustment(normal.pcl = experiment$CTRL, tumor.pcl = experiment$TEST, normalname = "The_healthy_controls", dataname = "The_effect_of_cancer", org.directory = getwd(), e=E,P=Pw,B=Bw); ################################################### ### code chunk number 4: part2 ################################################### TTMAP_part1_hda <- TTMap::hyperrectangle_deviation_assessment(x = TTMAP_part1prime,k=dim(TTMAP_part1prime$Normal.mat)[2], dataname = "The_effect_of_cancer", normalname = "The_healthy_controls"); head(TTMAP_part1_hda$Dc.Dmat) ################################################### ### code chunk number 5: part3 ################################################### library(rgl) ALPHA <- 1 annot <- c(paste(colnames(experiment$TEST[,-seq_len(3)]),"Dis",sep=".") ,paste(colnames(experiment$CTRL[,-seq_len(3)]),"Dis",sep=".")) annot <- cbind(annot,annot) rownames(annot)<-annot[,1] dd5_sgn_only <-TTMap::generate_mismatch_distance(TTMAP_part1_hda, select=rownames(TTMAP_part1_hda$Dc.Dmat),alpha = ALPHA) TTMAP_part2_gtlmap <- TTMap::ttmap(TTMAP_part1_hda,TTMAP_part1_hda$m, select=rownames(TTMAP_part1_hda$Dc.Dmat), annot,e= TTMap::calcul_e(dd5_sgn_only,0.95,TTMAP_part1prime,1), filename="first_comparison", n=1,dd=dd5_sgn_only) rgl.postscript("first_output.pdf","pdf") ################################################### ### code chunk number 6: part4 ################################################### TTMap::ttmap_sgn_genes(TTMAP_part2_gtlmap, TTMAP_part1_hda, TTMAP_part1prime, annot, n = 2, a = ALPHA, filename = "first_trial", annot = TTMAP_part1prime$tag.pcl, col = "NAME", path = getwd(), Relaxed = 0)