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1 # 1-20-10 Qunhua Li
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2 #
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3 # This program first plots correspondence curve and IDR threshold plot
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4 # (i.e. number of selected peaks vs IDR) for each pair of sample
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5 #
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6 # usage:
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7 # Rscript batch-consistency-plot-merged.r [script_path] [npairs] [output.dir] [input.file.prefix 1, 2, 3 ...]
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8 # [npairs]: integer, number of consistency analyses
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9 # (e.g. if 2 replicates, npairs=1, if 3 replicates, npairs=3
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10 # [output.prefix]: output directory and file name prefix for plot eg. /plots/idrPlot
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11 # [input.file.prefix 1, 2, 3]: prefix for the output from batch-consistency-analysis2. They are the input files for merged analysis see below for examples (i.e. saved.file.prefix). It can be multiple files
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12 #
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13
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14 args <- commandArgs(trailingOnly=T)
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15 script_path <- args[1]
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16 npair <- args[2] # number of curves to plot on the same figure
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17 output.file.prefix <- args[3] # file name for plot, generated from script at the outer level
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18 df.txt <- 10
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19 ntemp <- as.numeric(npair)
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20 saved.file.prefix <- list() # identifier of filenames that contain the em and URI results
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21 source(paste(script_path, "/functions-all-clayton-12-13.r", sep=""))
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22
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23 uri.list <- list()
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24 uri.list.match <- list()
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25 ez.list <- list()
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26 legend.txt <- c()
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27 em.output.list <- list()
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28 uri.output.list <- list()
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29
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30 for(i in 1:npair){
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31 saved.file.prefix[i] <- args[3+i]
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32
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33 load(paste(saved.file.prefix[i], "-uri.sav", sep=""))
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34 load(paste(saved.file.prefix[i], "-em.sav", sep=""))
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35
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36 uri.output.list[[i]] <- uri.output
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37 em.output.list[[i]] <- em.output
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38
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39 ez.list[[i]] <- get.ez.tt.all(em.output, uri.output.list[[i]]$data12.enrich$merge1,
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40 uri.output.list[[i]]$data12.enrich$merge2) # reverse =T for error rate
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41
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42 # URI for all peaks
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43 uri.list[[i]] <- uri.output$uri.n
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44 # URI for matched peaks
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45 uri.match <- get.uri.matched(em.output$data.pruned, df=df.txt)
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46 uri.list.match[[i]] <- uri.match$uri.n
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47
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48 file.name <- unlist(strsplit(as.character(saved.file.prefix[i]), "/"))
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49
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50 legend.txt[i] <- paste(i, "=", file.name[length(file.name)])
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51
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52 }
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53
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54 plot.uri.file <- paste(output.file.prefix, "-plot.ps", sep="")
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55
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56 ############# plot and report output
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57 # plot correspondence curve for each pair,
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58 # plot number of selected peaks vs IDR
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59 # plot all into 1 file
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60 postscript(paste(output.file.prefix, "-plot.ps", sep=""))
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61 par(mfcol=c(2,3), mar=c(5,6,4,2)+0.1)
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62 plot.uri.group(uri.list, NULL, file.name=NULL, c(1:npair), title.txt="all peaks")
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63 plot.uri.group(uri.list.match, NULL, file.name=NULL, c(1:npair), title.txt="matched peaks")
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64 plot.ez.group(ez.list, plot.dir=NULL, file.name=NULL, legend.txt=c(1:npair), y.lim=c(0, 0.6))
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65 plot(0, 1, type="n", xlim=c(0,1), ylim=c(0,1), xlab="", ylab="", xaxt="n", yaxt="n") # legends
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66 legend(0, 1, legend.txt, cex=0.6)
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67
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68 dev.off()
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69
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