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comparison ChipSeqRatioAnalysis.R @ 5:378565f5a875 draft

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author petr-novak
date Fri, 22 Nov 2019 07:56:48 -0500
parents e320ef2d105a
children f224513123a1
comparison
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4:d397f5a85464 5:378565f5a875
1 #!/usr/bin/env Rscript 1 #!/usr/bin/env Rscript
2 library(R2HTML, quietly=T) 2 library(R2HTML, quietly=T)
3 library(base64enc, quietly=T) 3 library(base64enc, quietly=T)
4 4
5 5
6 htmlheader=" 6 htmlheader=
7 <html xmlns:mml=\"http://www.w3.org/1998/Math/MathML\"> 7 " <html xmlns:mml=\"http://www.w3.org/1998/Math/MathML\">
8 <head> 8 <head>
9 <title> ChIP-Seq Mapper Output </title> 9 <title> ChIP-Seq Mapper Output </title>
10 <style> 10 <style>
11 <!-- 11 html,body{font-family:Verdana,sans-serif;font-size:15px;line-height:1.5}
12 table { background:#FFFFFF;
13 border:1px solid gray;
14 border-collapse:collapse;
15 color:#fff;
16 font:normal 13px verdana, arial, helvetica, sans-serif;
17 width: 100%;
18 12
19 } 13 table {
20 caption { border:1px solid #5C443A; 14 border-collapse: collapse;
21 color:#5C443A; 15 border: 1px solid black;
22 font-weight:bold; 16 width: 1000pt
23 font-size:20pt 17 }
24 padding:6px 4px 8px 0px; 18 table, th, td {
25 text-align:center; 19 border: 1px solid black;
26 20 }
27 } 21 </style>
28 td, th { color:#363636;
29 padding:.4em;
30 }
31 tr { border:1px dotted gray;
32 }
33 thead th, tfoot th { background:#5C443A;
34 color:#FFFFFF;
35 padding:3px 10px 3px 10px;
36 text-align:left;
37 text-transform:uppercase;
38 }
39 tbody td a { color:#3636FF;
40 text-decoration:underline;
41 }
42 tbody td a:visited { color:gray;
43 text-decoration:line-through;
44 }
45 tbody td a:hover { text-decoration:underline;
46 }
47 tbody th a { color:#3636FF;
48 font-weight:normal;
49 text-decoration:none;
50 }
51 tbody th a:hover { color:#363636;
52 }
53 tbody td+td+td+td a { background-image:url('bullet_blue.png');
54 background-position:left center;
55 background-repeat:no-repeat;
56 color:#FFFFFF;
57 padding-left:15px;
58 }
59 tbody td+td+td+td a:visited { background-image:url('bullet_white.png');
60 background-position:left center;
61 background-repeat:no-repeat;
62 }
63 tbody th, tbody td { text-align:left;
64 vertical-align:top;
65 }
66 tfoot td { background:#5C443A;
67 color:#FFFFFF;
68 padding-top:3px;
69 }
70 .odd { background:#fff;
71 }
72 tbody tr:hover { background:#EEEEEE;
73 border:1px solid #03476F;
74 color:#000000;
75 }
76 -->
77 </style>
78 22
79 </head> 23 </head>
80 24
81 " 25
26
27 "
82 28
83 29
84 #arguments 30 #arguments
85 args <- commandArgs(trailingOnly = TRUE) 31 args <- commandArgs(trailingOnly = TRUE)
86 input <- args[1] 32 input <- args[1]
95 df$"Normalized ratio Chip/Input"=(df$Chip_Hits/chipN)/(df$Input_Hits/inputN) 41 df$"Normalized ratio Chip/Input"=(df$Chip_Hits/chipN)/(df$Input_Hits/inputN)
96 42
97 df$"Ratio Chip/(Chip+Input)"=df$Chip_Hits/(df$Chip_Hits + df$Input_Hits) 43 df$"Ratio Chip/(Chip+Input)"=df$Chip_Hits/(df$Chip_Hits + df$Input_Hits)
98 df$"Normalized ratio Chip/(Chip+Input)"=(df$Chip_Hits/chipN)/((df$Input_Hits/inputN)+(df$Chip_Hits/chipN)) 44 df$"Normalized ratio Chip/(Chip+Input)"=(df$Chip_Hits/chipN)/((df$Input_Hits/inputN)+(df$Chip_Hits/chipN))
99 45
100 outputTable = df[df$"Normalized ratio Chip/(Chip+Input)" > threshld,] 46 outputTable = df[df$"Normalized ratio Chip/(Chip+Input)" > threshld,
101 outputTable = outputTable[!is.na(outputTable$Cluster),] 47 ]
48 outputTable = outputTable[!is.na(outputTable$Cluster),
49 c('Cluster', 'Chip_Hits', 'Input_Hits',
50 'Normalized ratio Chip/Input','Normalized ratio Chip/(Chip+Input)')]
102 save.image("tmp.RData") #Plot creation 51 save.image("tmp.RData") #Plot creation
103 pngfile <- tempfile() 52 pngfile <- tempfile()
104 png(pngfile, width = 1000, height = 1200, pointsize=20) 53 png(pngfile, width = 1000, height = 1200, pointsize=20)
105 par(mfrow=c(3,1)) 54 par(mfrow=c(2,1))
106 lims=range(df$"Normalized ratio Chip/Input"[df$"Normalized ratio Chip/Input">0], finite = TRUE) 55 lims=range(df$"Normalized ratio Chip/Input"[df$"Normalized ratio Chip/Input">0], finite = TRUE)
107 suppressWarnings(plot(df$Cluster,df$"Normalized ratio Chip/Input", log="y", xlab="Cluster Nr.", ylab="Normalized ChiP/Seq ratio", pch=20, ylim=lims)) 56 suppressWarnings(plot(df$Cluster,df$"Normalized ratio Chip/Input", log="y", xlab="Cluster Nr.", ylab="Normalized ChiP/Seq ratio", pch=20, ylim=lims))
108 abline(h=1,col='#00000080', lwd = 2) 57 abline(h=1,col='#00000080', lwd = 2)
109 abline(h=2,col='#FF000080', lwd = 2) 58 abline(h=2,col='#FF000080', lwd = 2)
110 59
111 lims=range(df$"Normalized ratio Chip/Input", finite = TRUE)
112 suppressWarnings(plot(df$Cluster,df$"Normalized ratio Chip/Input", xlab="Cluster Nr.", ylab="Normalize ChiP/Seq ratio", pch=20, ylim=lims))
113 abline(h=1,col='#00000080', lwd = 2)
114 abline(h=2,col='#FF000080', lwd = 2)
115 60
116 suppressWarnings(plot(df$Cluster,df$"Normalized ratio Chip/(Chip+Input)", xlab="Cluster Nr.", ylab="Normalized Chip/(Chip+Input)", pch=20)) 61 suppressWarnings(plot(df$Cluster,df$"Normalized ratio Chip/(Chip+Input)", xlab="Cluster Nr.", ylab="Normalized Chip/(Chip+Input)", pch=20))
117 abline(h=0.5,col='#00000080', lwd = 2) 62 abline(h=0.5,col='#00000080', lwd = 2)
118 abline(h=threshld,col='#FF000080', lwd = 2) 63 abline(h=threshld,col='#FF000080', lwd = 2)
119 64
131 cat(htmlheader, file = filename) 76 cat(htmlheader, file = filename)
132 77
133 78
134 HTML(graph, file=filename) 79 HTML(graph, file=filename)
135 if (nrow(outputTable)>0){ 80 if (nrow(outputTable)>0){
136 HTML(outputTable, file=filename, classtable = "dataframe", row.names=FALSE, Align='left') 81 HTML(outputTable, file=filename, classtable = "dataframe",
82 row.names=FALSE, align='left', caption="Clusters with Normalized ChIP/Input ratio > 2", captionalign="top")
137 } 83 }
138 HTMLEndFile(filename) 84 HTMLEndFile(filename)
139 file.rename(from=filename, to=HTMLfile) 85 file.rename(from=filename, to=HTMLfile)
140 write.table(df, file=input, sep="\t", row.names = FALSE) 86 write.table(df, file=input, sep="\t", row.names = FALSE)