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1 #!/usr/bin/env Rscript
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2 library(R2HTML, quietly=T)
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3 library(base64enc, quietly=T)
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4
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5
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5
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6 htmlheader=
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7 " <html xmlns:mml=\"http://www.w3.org/1998/Math/MathML\">
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3
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8 <head>
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9 <title> ChIP-Seq Mapper Output </title>
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5
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10 <style>
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11 html,body{font-family:Verdana,sans-serif;font-size:15px;line-height:1.5}
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12
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13 table {
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14 border-collapse: collapse;
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15 border: 1px solid black;
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16 width: 1000pt
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17 }
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18 table, th, td {
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19 border: 1px solid black;
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20 }
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21 </style>
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22
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23 </head>
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24
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25
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26
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27 "
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3
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28
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29
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30 #arguments
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31 args <- commandArgs(trailingOnly = TRUE)
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32 input <- args[1]
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33 HTMLfile <- args[2]
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8
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34 thr = 5
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35 threshld <- thr/(thr+1)
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36
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3
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37 inputN=as.numeric(args[3])
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38 chipN=as.numeric(args[4])
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39 #dataframe preprocessing and table creation
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40 df <- read.delim(input, comment.char="#")
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41
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42 df$"Ratio Chip/Input"=df$Chip_Hits/df$Input_Hits
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43 df$"Normalized ratio Chip/Input"=(df$Chip_Hits/chipN)/(df$Input_Hits/inputN)
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44
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45 df$"Ratio Chip/(Chip+Input)"=df$Chip_Hits/(df$Chip_Hits + df$Input_Hits)
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46 df$"Normalized ratio Chip/(Chip+Input)"=(df$Chip_Hits/chipN)/((df$Input_Hits/inputN)+(df$Chip_Hits/chipN))
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47
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48 outputTable = df[df$"Normalized ratio Chip/(Chip+Input)" > threshld,
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49 ]
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50 outputTable = outputTable[!is.na(outputTable$Cluster),
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51 c('Cluster', 'Chip_Hits', 'Input_Hits',
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52 'Normalized ratio Chip/Input','Normalized ratio Chip/(Chip+Input)')]
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53 save.image("tmp.RData") #Plot creation
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54 pngfile <- tempfile()
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55 png(pngfile, width = 1000, height = 1200, pointsize=20)
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56 par(mfrow=c(2,1))
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57 lims=range(df$"Normalized ratio Chip/Input"[df$"Normalized ratio Chip/Input">0], finite = TRUE)
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58 suppressWarnings(plot(df$Cluster,df$"Normalized ratio Chip/Input", log="y", xlab="Cluster Nr.", ylab="Normalized ChiP/Input ratio", pch=20, ylim=lims))
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59 abline(h=1,col='#00000080', lwd = 2)
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60 abline(h=thr,col='#FF000080', lwd = 2)
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61
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62
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63 suppressWarnings(plot(df$Cluster,df$"Normalized ratio Chip/(Chip+Input)", xlab="Cluster Nr.", ylab="Normalized Chip/(Chip+Input)", pch=20))
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64 abline(h=0.5,col='#00000080', lwd = 2)
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65 abline(h=threshld,col='#FF000080', lwd = 2)
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66
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67
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68 dev.off()
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69 graph <- paste('<img src="data:image/png;base64 ,',
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70 base64encode(pngfile),
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71 '" alt="image" />'
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72 )
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73
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74 #HMTL report creation + writing final output
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75 directory=dirname(HTMLfile)
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76 filename=basename(HTMLfile)
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77 ## create HTML header
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78 cat(htmlheader, file = filename)
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79
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80
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81 HTML(graph, file=filename)
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82 if (nrow(outputTable)>0){
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83 HTML(outputTable, file=filename, classtable = "dataframe",
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84 row.names=FALSE, align='left', caption=paste("Clusters with Normalized ChIP/Input ratio >", thr), captionalign="top")
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85 }
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86 HTMLEndFile(filename)
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87 # file.rename(from=filename, to=HTMLfile)
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88 system(sprintf("cp -r ./%s %s", filename, HTMLfile))
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89 write.table(df, file=input, sep="\t", row.names = FALSE)
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