inst/doc/uSORT_quick_start.R

In uSORT: uSORT: A self-refining ordering pipeline for gene selection

## -----------------------------------------------------------------------------
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()