Mercurial > repos > davidvanzessen > argalaxy_tools
diff report_clonality/naive_gene_freq.htm @ 27:b539aeb75980 draft
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| author | davidvanzessen |
|---|---|
| date | Tue, 28 Feb 2017 08:10:34 -0500 |
| parents | 5d11c9139a55 |
| children | 4d2a8f98a502 |
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--- a/report_clonality/naive_gene_freq.htm Mon Feb 13 09:08:46 2017 -0500 +++ b/report_clonality/naive_gene_freq.htm Tue Feb 28 08:10:34 2017 -0500 @@ -1,103 +1,217 @@ -<html> +<html xmlns:v="urn:schemas-microsoft-com:vml" +xmlns:o="urn:schemas-microsoft-com:office:office" +xmlns:w="urn:schemas-microsoft-com:office:word" +xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" +xmlns="http://www.w3.org/TR/REC-html40"> <head> <meta http-equiv=Content-Type content="text/html; charset=windows-1252"> -<meta name=Generator content="Microsoft Word 14 (filtered)"> +<meta name=ProgId content=Word.Document> +<meta name=Generator content="Microsoft Word 14"> +<meta name=Originator content="Microsoft Word 14"> +<link rel=File-List href="Gene%20frequencies%20tab_files/filelist.xml"> +<link rel=themeData href="Gene%20frequencies%20tab_files/themedata.thmx"> <style> <!-- /* Font Definitions */ @font-face {font-family:Calibri; - panose-1:2 15 5 2 2 2 4 3 2 4;} + panose-1:2 15 5 2 2 2 4 3 2 4; + mso-font-charset:0; 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+ mso-bidi-font-size:10.0pt; + mso-ascii-font-family:Calibri; + mso-hansi-font-family:Calibri;} .MsoPapDefault - {margin-bottom:10.0pt; + {mso-style-type:export-only; + margin-bottom:10.0pt; line-height:115%;} @page WordSection1 {size:8.5in 11.0in; - margin:1.0in 1.0in 1.0in 1.0in;} + margin:1.0in 1.0in 1.0in 1.0in; + mso-header-margin:.5in; + mso-footer-margin:.5in; + mso-paper-source:0;} div.WordSection1 {page:WordSection1;} --> </style> - +<!--[if gte mso 10]> +<style> + /* Style Definitions */ + table.MsoNormalTable + {mso-style-name:"Table Normal"; + mso-tstyle-rowband-size:0; + mso-tstyle-colband-size:0; + mso-style-noshow:yes; + mso-style-priority:99; + mso-style-parent:""; + mso-padding-alt:0in 5.4pt 0in 5.4pt; + mso-para-margin-top:0in; + mso-para-margin-right:0in; + mso-para-margin-bottom:10.0pt; + mso-para-margin-left:0in; + line-height:115%; + mso-pagination:widow-orphan; + font-size:10.0pt; + font-family:"Calibri","sans-serif";} +</style> +<![endif]--><!--[if gte mso 9]><xml> + <o:shapedefaults v:ext="edit" spidmax="1026"/> +</xml><![endif]--><!--[if gte mso 9]><xml> + <o:shapelayout v:ext="edit"> + <o:idmap v:ext="edit" data="1"/> + </o:shapelayout></xml><![endif]--> </head> -<body lang=EN-US> +<body lang=EN-US style='tab-interval:.5in'> <div class=WordSection1> +<p class=MsoNoSpacing style='text-align:justify'><b><u><span lang=EN-GB +style='font-size:12.0pt;font-family:"Times New Roman","serif";mso-ansi-language: +EN-GB'>Gene frequencies tab</span></u></b></p> + <p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;text-align: justify;line-height:normal'><span lang=EN-GB style='font-size:12.0pt; -font-family:"Times New Roman","serif"'>This tab gives information on the -frequency of V, D and J gene usage. </span></p> +font-family:"Times New Roman","serif";mso-ansi-language:EN-GB'>This tab gives +information on the frequency of V, D and J gene usage. <o:p></o:p></span></p> + +<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;text-align: +justify;line-height:normal'><o:p> </o:p></p> -<p class=MsoNoSpacingCxSpMiddle style='text-align:justify'><b><span lang=EN-GB -style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Graphs</span></b></p> +<p class=MsoNoSpacing style='text-align:justify'><b><span lang=EN-GB +style='font-size:12.0pt;font-family:"Times New Roman","serif";mso-ansi-language: +EN-GB'>Graphs</span></b></p> -<p class=MsoNormalCxSpFirst style='margin-bottom:0in;margin-bottom:.0001pt; -text-align:justify;line-height:normal'><u><span lang=EN-GB style='font-size: -12.0pt;font-family:"Times New Roman","serif"'>Distribution of V gene families</span></u></p> +<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;text-align: +justify;line-height:normal'><u><span lang=EN-GB style='font-size:12.0pt; +font-family:"Times New Roman","serif";mso-ansi-language:EN-GB'>Distribution of +V gene families<o:p></o:p></span></u></p> -<p class=MsoNormalCxSpMiddle style='margin-bottom:0in;margin-bottom:.0001pt; -text-align:justify;line-height:normal'><a name="OLE_LINK123"></a><a -name="OLE_LINK122"></a><a name="OLE_LINK121"><span lang=EN-GB style='font-size: -12.0pt;font-family:"Times New Roman","serif"'>Bar graph showing the frequency -of V gene family usage in all uploaded donors. </span></a></p> +<p class=MsoNoSpacing style='text-align:justify'><a name="OLE_LINK121"></a><a +name="OLE_LINK123"></a><a name="OLE_LINK122"></a><span style='mso-bookmark: +OLE_LINK121'><span lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"; +mso-ansi-language:EN-GB'>Bar graph showing the frequency of V gene family usage +in all uploaded donors. </span></span><span lang=EN-GB style='font-size:12.0pt; +font-family:"Times New Roman","serif";mso-ansi-language:EN-GB'><o:p></o:p></span></p> + +<p class=MsoNoSpacing style='text-align:justify'><o:p> </o:p></p> -<p class=MsoNormalCxSpMiddle style='margin-bottom:0in;margin-bottom:.0001pt; -text-align:justify;line-height:normal'><u><span lang=EN-GB style='font-size: -12.0pt;font-family:"Times New Roman","serif"'>Relative frequency of V gene -usage</span></u></p> +<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;text-align: +justify;line-height:normal'><u><span lang=EN-GB style='font-size:12.0pt; +font-family:"Times New Roman","serif";mso-ansi-language:EN-GB'>Relative +frequency of V gene usage<o:p></o:p></span></u></p> + +<p class=MsoNoSpacing style='text-align:justify'><a name="OLE_LINK124"></a><a +name="OLE_LINK126"></a><a name="OLE_LINK125"></a><span style='mso-bookmark: +OLE_LINK124'><span lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"; +mso-ansi-language:EN-GB'>Bar graph showing the frequency of V genes in all +uploaded donors. The order of the V genes on the x-axis can be altered by +altering the “<span style='color:black;background:white'>Order of V(D)J genes +in graphs” filter on the main page of the Immune repertoire pipeline.</span></span></span><span +lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"; +color:black;background:white;mso-ansi-language:EN-GB'><o:p></o:p></span></p> -<p class=MsoNormalCxSpLast style='margin-bottom:0in;margin-bottom:.0001pt; -text-align:justify;line-height:normal'><a name="OLE_LINK126"></a><a -name="OLE_LINK125"></a><a name="OLE_LINK124"><span lang=EN-GB style='font-size: -12.0pt;font-family:"Times New Roman","serif"'>Bar graph showing the frequency -of V genes in all uploaded donors. The order of the V genes on the x-axis can -be altered by altering the “<span style='color:black;background:white'>Order of -V(D)J genes in graphs” filter on the main page of the Immune repertoire -pipeline.</span></span></a></p> +<p class=MsoNoSpacing style='text-align:justify'><o:p> </o:p></p> + +<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;text-align: +justify;line-height:normal'><u><span lang=EN-GB style='font-size:12.0pt; +font-family:"Times New Roman","serif";mso-ansi-language:EN-GB'>Relative +frequency of D gene usage<o:p></o:p></span></u></p> -<p class=MsoNoSpacingCxSpLast style='text-align:justify'><a name="OLE_LINK129"></a><a -name="OLE_LINK128"></a><a name="OLE_LINK127"><u><span lang=EN-GB -style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Relative -frequency of D gene usage</span></u></a></p> +<p class=MsoNoSpacing style='text-align:justify'><span lang=EN-GB +style='font-size:12.0pt;font-family:"Times New Roman","serif";mso-ansi-language: +EN-GB'>Bar graph showing the frequency of D genes in all uploaded donors. The +order of the D genes on the x-axis can be altered by altering the “<span +style='color:black;background:white'>Order of V(D)J genes in graphs” filter on +the main page of the Immune repertoire pipeline.<o:p></o:p></span></span></p> + +<p class=MsoNoSpacing style='text-align:justify'><o:p> </o:p></p> -<p class=MsoNormalCxSpFirst style='margin-bottom:0in;margin-bottom:.0001pt; -text-align:justify;line-height:normal'><span lang=EN-GB style='font-size:12.0pt; -font-family:"Times New Roman","serif"'>Bar graph showing the frequency of D -genes in all uploaded donors. The order of the D genes on the x-axis can be -altered by altering the “<span style='color:black;background:white'>Order of -V(D)J genes in graphs” filter on the main page of the Immune repertoire -pipeline.</span></span></p> +<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;text-align: +justify;line-height:normal'><u><span lang=EN-GB style='font-size:12.0pt; +font-family:"Times New Roman","serif";mso-ansi-language:EN-GB'>Relative +frequency of J gene usage<o:p></o:p></span></u></p> -<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB -style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Relative -frequency of J gene usage</span></u></p> +<p class=MsoNoSpacing style='text-align:justify'><span lang=EN-GB +style='font-size:12.0pt;font-family:"Times New Roman","serif";mso-ansi-language: +EN-GB'>Bar graph showing the frequency of J genes in all uploaded donors. The +order of the J genes on the x-axis can be altered by altering the “<span +style='color:black;background:white'>Order of V(D)J genes in graphs” filter on +the main page of the Immune repertoire pipeline.<o:p></o:p></span></span></p> + +<p class=MsoNoSpacing style='text-align:justify'><o:p> </o:p></p> -<p class=MsoNormalCxSpFirst style='margin-bottom:0in;margin-bottom:.0001pt; -text-align:justify;line-height:normal'><span lang=EN-GB style='font-size:12.0pt; -font-family:"Times New Roman","serif"'>Bar graph showing the frequency of J -genes in all uploaded donors. The order of the J genes on the x-axis can be -altered by altering the “<span style='color:black;background:white'>Order of -V(D)J genes in graphs” filter on the main page of the Immune repertoire -pipeline.</span></span></p> +<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;text-align: +justify;line-height:normal'><u><span style='font-size:12.0pt;font-family:"Times New Roman","serif"'>D +reading frame<o:p></o:p></span></u></p> + +<p class=MsoNoSpacing style='text-align:justify'><span lang=EN-GB +style='font-size:12.0pt;font-family:"Times New Roman","serif";mso-ansi-language: +EN-GB'>Bar graph visualizing the frequency by which each D reading frame is +used in each donor.</span></p> </div>