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3
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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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6 htmlheader="
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7 <html xmlns:mml=\"http://www.w3.org/1998/Math/MathML\">
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8 <head>
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9 <title> ChIP-Seq Mapper Output </title>
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10 <style>
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11 <!--
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12 table { background:#FFFFFF;
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13 border:1px solid gray;
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14 border-collapse:collapse;
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15 color:#fff;
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16 font:normal 13px verdana, arial, helvetica, sans-serif;
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17 width: 100%;
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18
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19 }
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20 caption { border:1px solid #5C443A;
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21 color:#5C443A;
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22 font-weight:bold;
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23 font-size:20pt
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24 padding:6px 4px 8px 0px;
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25 text-align:center;
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26
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27 }
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28 td, th { color:#363636;
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29 padding:.4em;
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30 }
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31 tr { border:1px dotted gray;
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32 }
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33 thead th, tfoot th { background:#5C443A;
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34 color:#FFFFFF;
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35 padding:3px 10px 3px 10px;
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36 text-align:left;
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37 text-transform:uppercase;
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38 }
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39 tbody td a { color:#3636FF;
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40 text-decoration:underline;
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41 }
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42 tbody td a:visited { color:gray;
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43 text-decoration:line-through;
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44 }
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45 tbody td a:hover { text-decoration:underline;
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46 }
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47 tbody th a { color:#3636FF;
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48 font-weight:normal;
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49 text-decoration:none;
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50 }
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51 tbody th a:hover { color:#363636;
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52 }
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53 tbody td+td+td+td a { background-image:url('bullet_blue.png');
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54 background-position:left center;
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55 background-repeat:no-repeat;
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56 color:#FFFFFF;
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57 padding-left:15px;
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58 }
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59 tbody td+td+td+td a:visited { background-image:url('bullet_white.png');
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60 background-position:left center;
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61 background-repeat:no-repeat;
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62 }
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63 tbody th, tbody td { text-align:left;
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64 vertical-align:top;
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65 }
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66 tfoot td { background:#5C443A;
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67 color:#FFFFFF;
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68 padding-top:3px;
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69 }
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70 .odd { background:#fff;
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71 }
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72 tbody tr:hover { background:#EEEEEE;
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73 border:1px solid #03476F;
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74 color:#000000;
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75 }
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76 -->
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77 </style>
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78
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79 </head>
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80
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81 "
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82
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83
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84 #arguments
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85 args <- commandArgs(trailingOnly = TRUE)
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86 input <- args[1]
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87 HTMLfile <- args[2]
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88 threshld <- 2/(2+1)
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89 inputN=as.numeric(args[3])
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90 chipN=as.numeric(args[4])
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91 #dataframe preprocessing and table creation
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92 df <- read.delim(input, comment.char="#")
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93
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94 df$"Ratio Chip/Input"=df$Chip_Hits/df$Input_Hits
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95 df$"Normalized ratio Chip/Input"=(df$Chip_Hits/chipN)/(df$Input_Hits/inputN)
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96
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97 df$"Ratio Chip/(Chip+Input)"=df$Chip_Hits/(df$Chip_Hits + df$Input_Hits)
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98 df$"Normalized ratio Chip/(Chip+Input)"=(df$Chip_Hits/chipN)/((df$Input_Hits/inputN)+(df$Chip_Hits/chipN))
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99
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100 outputTable = df[df$"Normalized ratio Chip/(Chip+Input)" > threshld,]
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101 outputTable = outputTable[!is.na(outputTable$Cluster),]
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102 save.image("tmp.RData") #Plot creation
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103 pngfile <- tempfile()
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104 png(pngfile, width = 1000, height = 1200, pointsize=20)
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105 par(mfrow=c(3,1))
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106 lims=range(df$"Normalized ratio Chip/Input"[df$"Normalized ratio Chip/Input">0], finite = TRUE)
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107 suppressWarnings(plot(df$Cluster,df$"Normalized ratio Chip/Input", log="y", xlab="Cluster Nr.", ylab="Normalized ChiP/Seq ratio", pch=20, ylim=lims))
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108 abline(h=1,col='#00000080', lwd = 2)
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109 abline(h=2,col='#FF000080', lwd = 2)
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110
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111 lims=range(df$"Normalized ratio Chip/Input", finite = TRUE)
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112 suppressWarnings(plot(df$Cluster,df$"Normalized ratio Chip/Input", xlab="Cluster Nr.", ylab="Normalize ChiP/Seq ratio", pch=20, ylim=lims))
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113 abline(h=1,col='#00000080', lwd = 2)
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114 abline(h=2,col='#FF000080', lwd = 2)
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115
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116 suppressWarnings(plot(df$Cluster,df$"Normalized ratio Chip/(Chip+Input)", xlab="Cluster Nr.", ylab="Normalized Chip/(Chip+Input)", pch=20))
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117 abline(h=0.5,col='#00000080', lwd = 2)
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118 abline(h=threshld,col='#FF000080', lwd = 2)
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119
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120
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121 dev.off()
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122 graph <- paste('<img src="data:image/png;base64 ,',
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123 base64encode(pngfile),
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124 '" alt="image" />'
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125 )
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126
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127 #HMTL report creation + writing final output
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128 directory=dirname(HTMLfile)
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129 filename=basename(HTMLfile)
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130 ## create HTML header
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131 cat(htmlheader, file = filename)
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132
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133
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134 HTML(graph, file=filename)
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135 if (nrow(outputTable)>0){
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136 HTML(outputTable, file=filename, classtable = "dataframe", row.names=FALSE, Align='left')
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137 }
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138 HTMLEndFile(filename)
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139 file.rename(from=filename, to=HTMLfile)
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140 write.table(df, file=input, sep="\t", row.names = FALSE)
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