## ----------------------------------------------------------------------------- require(uSORT) # uSORT_GUI() ## ---- eval=TRUE--------------------------------------------------------------- args(uSORT) ## ---- eval=TRUE--------------------------------------------------------------- dir <- system.file('extdata', package='uSORT') file <- list.files(dir, pattern='.txt$', full=TRUE) # uSORT_results <- uSORT(exprs_file = file, # log_transform = TRUE, # remove_outliers = TRUE, # project_name = "uSORT_example", # preliminary_sorting_method = "autoSPIN", # refine_sorting_method = "sWanderlust", # result_directory = getwd(), # save_results = TRUE, # reproduce_seed = 1234) ## ---- eval=TRUE--------------------------------------------------------------- #str(uSORT_results) # List of 7 # $ exp_raw : num [1:251, 1:43280] 1.08 0 0 0.62 0 0 0 0.27 1.16 0 ... # ..- attr(*, "dimnames")=List of 2 # .. ..$ : chr [1:251] "RMD119" "RMD087" "RMD078" "RMD225" ... # .. ..$ : chr [1:43280] "0610005C13Rik" "0610007P14Rik" "0610009B22Rik" "0610009E02Rik" ... # $ trimmed_log2exp : num [1:241, 1:9918] 4.82 0 0 2.77 5.84 ... # ..- attr(*, "dimnames")=List of 2 # .. ..$ : chr [1:241] "RMD119" "RMD087" "RMD078" "RMD225" ... # .. ..$ : chr [1:9918] "0610007P14Rik" "0610009B22Rik" "0610009E02Rik" "0610009O20Rik" ... # $ preliminary_sorting_genes : chr [1:650] "1110038B12Rik" "1190002F15Rik" "2810417H13Rik" "5430435G22Rik" ... # $ preliminary_sorting_order : chr [1:241] "RMD196" "RMD236" "RMD250" "RMD220" ... # $ refined_sorting_genes : chr [1:320] "Mpo" "H2-Aa" "Cd74" "H2-Ab1" ... # $ refined_sorting_order : chr [1:241] "RMD271" "RMD272" "RMD265" "RMD295" ... # $ driverGene_refinedOrder_log2exp: num [1:241, 1:320] 13.16 10.77 12.17 9.82 9.77 ... # ..- attr(*, "dimnames")=List of 2 # .. ..$ : chr [1:241] "RMD271" "RMD272" "RMD265" "RMD295" ... # .. ..$ : chr [1:320] "Mpo" "H2-Aa" "Cd74" "H2-Ab1" ... ## ---- eval=TRUE--------------------------------------------------------------- # sig_genes <- read.table(file.path(system.file('extdata', package='uSORT'), 'signature_genes.txt')) # sig_genes <- as.character(sig_genes[,1]) # spl_annotat <- read.table(file.path(system.file('extdata', package='uSORT'), 'celltype.txt'),header=T) ## ---- eval=FALSE-------------------------------------------------------------- # pre_log2ex <- uSORT_results$trimmed_log2exp[rev(uSORT_results$preliminary_sorting_order), ] # m <- spl_annotat[match(rownames(pre_log2ex), spl_annotat$SampleID), ] # celltype_color <- c('blue','red','black') # celltype <- c('MDP','CDP','PreDC') # cell_color <- celltype_color[match(m$GroupID, celltype)] # sigGenes_log2ex <- t(pre_log2ex[ ,colnames(pre_log2ex) %in% sig_genes]) # fileNm <- paste0(project_name, '_signatureGenes_profiles_preliminary.pdf') # heatmap.2(as.matrix(sigGenes_log2ex), # dendrogram='row', # trace='none', # col = bluered, # Rowv=T,Colv=F, # scale = 'row', # cexRow=1.8, # ColSideColors=cell_color, # margins = c(8, 8)) # # legend("topright", # legend=celltype, # col=celltype_color, # pch=20, # horiz=T, # bty= "n", # inset=c(0,-0.01), # pt.cex=1.5) ## ---- eval=FALSE-------------------------------------------------------------- # ref_log2ex <- uSORT_results$trimmed_log2exp[uSORT_results$refined_sorting_order, ] # m <- spl_annotat[match(rownames(ref_log2ex), spl_annotat$SampleID), ] # celltype_color <- c('blue','red','black') # celltype <- c('MDP','CDP','PreDC') # cell_color <- celltype_color[match(m$GroupID, celltype)] # sigGenes_log2ex <- t(ref_log2ex[ ,colnames(ref_log2ex) %in% sig_genes]) # fileNm <- paste0(project_name, '_signatureGenes_profiles_refine.pdf') # heatmap.2(as.matrix(sigGenes_log2ex), # dendrogram='row', # trace='none', # col = bluered, # Rowv=T,Colv=F, # scale = 'row', # cexRow=1.8, # ColSideColors=cell_color, # margins = c(8, 8)) # # legend("topright", # legend=celltype, # col=celltype_color, # pch=20, # horiz=T, # bty= "n", # inset=c(0,-0.01), # pt.cex=1.5) ## ----------------------------------------------------------------------------- sessionInfo()