Mercurial > repos > lecorguille > xcms_summary

comparison xcms_summary.r @ 4:1245c04eebde draft

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planemo upload
author lecorguille
date Mon, 22 Feb 2016 17:07:53 -0500
parents 89a8b5ff3e44
children 11df21afc204
comparison
equal deleted inserted replaced
3:89a8b5ff3e44 4:1245c04eebde
40 40
41 # if the RData come from CAMERA 41 # if the RData come from CAMERA
42 if (!exists("xset") & exists("xa")) xset=xa@xcmsSet 42 if (!exists("xset") & exists("xa")) xset=xa@xcmsSet
43 43
44 # retrocompatability 44 # retrocompatability
45 if (!exists("sampleNamesList")) sampleNamesList=list("sampleNamesMakeNames"=make.names(sampnames(xset))) 45 if (!exists("sampleNamesList")) sampleNamesList=List("sampleNamesMakeNames"=make.names(sampnames(xset)))
46 46
47 if (!exists("xset")) stop("You need at least a xset or a xa object.") 47 if (!exists("xset")) stop("You need at least a xset or a xa object.")
48 48
49 49
50 50
75 } 75 }
76 writehtml("</div>") 76 writehtml("</div>")
77 77
78 writehtml("<h2>Samples used:</h2>") 78 writehtml("<h2>Samples used:</h2>")
79 writehtml("<div><table>") 79 writehtml("<div><table>")
80 if (all(sampnames(xset) == sampleNamesList$sampleNamesMakeNames)) { 80 if (all(sampnames(xset) != sampleNamesList$sampleNamesMakeNames)) {
81 sampleNameHeaderHtml = paste("<th>sample</th>") 81 sampleNameHeaderHtml = paste("<th>sample</th>")
82 sampleNameHtml = paste("<td>",sampnames(xset),"</td>") 82 sampleNameHtml = paste("<td>",sampnames(xset),"</td>")
83 } else { 83 } else {
84 sampleNameHeaderHtml = paste("<th>sample</th><th>sample renamed</th>") 84 sampleNameHeaderHtml = paste("<th>sample</th><th>sample renamed</th>")
85 sampleNameHtml = paste("<td>",sampnames(xset),"</td><td>",sampleNamesList$sampleNamesMakeNames,"</td>") 85 sampleNameHtml = paste("<td>",sampnames(xset),"</td><td>",sampleNamesList$sampleNamesMakeNames,"</td>")
87 87
88 if (!exists("md5sumList")) { 88 if (!exists("md5sumList")) {
89 md5sumHeaderHtml = "" 89 md5sumHeaderHtml = ""
90 md5sumHtml = "" 90 md5sumHtml = ""
91 md5sumLegend="" 91 md5sumLegend=""
92 } else if (is.null(md5sumList$removalBadCharacters)) { 92 } else if (!is.null(md5sumList$removalBadCharacters)) {
93 md5sumHeaderHtml = paste("<th>md5sum<sup>*</sup></th>") 93 md5sumHeaderHtml = paste("<th>md5sum<sup>*</sup></th>")
94 md5sumHtml = paste("<td>",md5sumList$origin,"</td>") 94 md5sumHtml = paste("<td>",md5sumList$origin,"</td>")
95 md5sumLegend = "<br/><sup>*</sup>The program md5sum is designed to verify data integrity. So you can check if the data were uploaded correctly or if the data were chancged during the process." 95 md5sumLegend = "<br/><sup>*</sup>The program md5sum is designed to verify data integrity. So you can check if the data were uploaded correctly or if the data were chancged during the process."
96 } else { 96 } else {
97 md5sumHeaderHtml = paste("<th>md5sum<sup>*</sup></th><th>md5sum<sup>**</sup> after bad characters removal</th>") 97 md5sumHeaderHtml = paste("<th>md5sum<sup>*</sup></th><th>md5sum<sup>**</sup> after bad characters removal</th>")
98 md5sumHtml = paste("<td>",md5sumList$origin,"</td><td>",md5sumList$removalBadCharacters,"</td>") 98 md5sumHtml = paste("<td>",md5sumList$origin,"</td><td>",md5sumList$origin,"</td>")
99 md5sumLegend = "<br/><sup>*</sup>The program md5sum is designed to verify data integrity. So you can check if the data were uploaded correctly or if the data were chancged during the process.<br/><sup>**</sup>Because some bad characters (eg: accent) were removed from your original file, the checksum have changed too.<br/>" 99 md5sumLegend = "<br/><sup>*</sup>The program md5sum is designed to verify data integrity. So you can check if the data were uploaded correctly or if the data were chancged during the process.<br/><sup>**</sup>Because some bad characters (eg: accent) were removed from your original file, the checksum have changed too.<br/>"
100 } 100 }
101 101
102 writehtml("<tr>",sampleNameHeaderHtml,"<th>filename</th>",md5sumHeaderHtml,"</tr>") 102 writehtml("<tr>",sampleNameHeaderHtml,"<th>filename</th>",md5sumHeaderHtml,"</tr>")
103 writehtml(paste("<tr>",sampleNameHtml,"<td>",xset@filepaths,"</td>",md5sumHtml,"</tr>")) 103 writehtml(paste("<tr>",sampleNameHtml,"<td>",xset@filepaths,"</td>",md5sumHtml,"</tr>"))