Template:F5samples: Difference between revisions
From FANTOM5_SSTAR
No edit summary |
mNo edit summary |
||
(15 intermediate revisions by the same user not shown) | |||
Line 1: | Line 1: | ||
{{Loading|loadingimage=sprites.gif}}<html> | {{Loading|loadingimage=sprites.gif}}<html> | ||
<style type="text/css" title="currentStyle"> | <style type="text/css" title="currentStyle"> | ||
@import "/5/sstar/rb_js/datatables | @import "/5/sstar/rb_js/html5button/datatables.css"; | ||
@import "/5/sstar/rb_js/datatables/extras/TableTools/media/css/TableTools.css"; | @import "/5/sstar/rb_js/datatables/extras/TableTools/media/css/TableTools.css"; | ||
</style> | </style> | ||
<script type="text/javascript" src="/5/sstar/rb_js/jquery-1.7.1.min.js"></script> | |||
<script type="text/javascript" src="/5/sstar/rb_js/html5button/datatables.js"></script> | |||
<script type="text/javascript" src="/5/sstar/rb_js/custom/expoconvert.js"></script> | <script type="text/javascript" src="/5/sstar/rb_js/custom/expoconvert.js"></script> | ||
<script type="text/javascript" language="javascript" src="/5/sstar/rb_js/datatables/extras/TableTools/media/js/TableTools.min.js"></script> | <script type="text/javascript" language="javascript" src="/5/sstar/rb_js/datatables/extras/TableTools/media/js/TableTools.min.js"></script> | ||
</html>{{#outerfile_existance: /5/sstar/sstar_img/f5samples/riken_cellimg/{{PAGENAME}}.jpg |<html> | </html>{{#outerfile_existance: /5/sstar/sstar_img/f5samples/riken_cellimg/{{PAGENAME}}.jpg |<html> | ||
Line 91: | Line 89: | ||
} | } | ||
/*"sDom": '<"top"i>rt<"bottom"flp><"clear">' */ | /*"sDom": '<"top"i>rt<"bottom"flp><"clear">' */ | ||
$('#ffcp_tf_enrichscore').DataTable( { | |||
data: mm_data, | |||
dom: 'Blfrtip', | |||
lengthMenu: [[10, 50, -1], [10, 50, "All"]], | |||
buttons: ['copyHtml5', 'excelHtml5', 'csvHtml5', 'pdfHtml5'], | |||
columnDefs: [{ targets: [1], visible: false}], | |||
columns: [ | |||
{ title: "CAGE peaks" , | |||
render: function ( data, type, row, meta ) { | |||
var peak_loc = row[0]; | |||
var peak_name = row[1]; | |||
return "<a href=\"/5/sstar/"+"FFCP_PHASE1:"+species+"::"+peak_loc +"\">"+peak_name+"</a>"; | |||
} | |||
}, | |||
{ title: "Log10(Relative expression over median)" }, | |||
{ title: "TPM" }, | |||
{ title: "TF." } | |||
], | |||
order: [[ 2, 'desc' ]] | |||
} ); | |||
}); | }); | ||
</script> | </script> | ||
<span id="tf_enrich_table_export_tool"></span> | <span id="tf_enrich_table_export_tool"></span> | ||
<table cellpadding="0" cellspacing="0" border="0" | <table cellpadding="0" cellspacing="0" border="0" id="ffcp_tf_enrichscore" class="stripe cell-border order-column compact"></table> | ||
</html> | </html> | ||
}} | }} | ||
<br><br>{{Fontsize|3|Co-expression clusters with enriched expression in this sample}}{{#info:Ranked list of co-expression cluster expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed. <br>Analyst:NA <br><br>link to dataset.<br>[http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters data]}}<html><script type="text/javascript"> | {{#vardefine:isHumanOrMouse|{{#switch:{{{sample_species}}}|Human (Homo sapiens)=1|Mouse (Mus musculus)=1|0}}}} | ||
{{#ifeq:{{#var:isHumanOrMouse}}|1|<br><br>{{Fontsize|3|Co-expression clusters with enriched expression in this sample}}{{#info:Ranked list of co-expression cluster expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed. <br>Analyst:NA <br><br>link to dataset.<br>[http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters data]}}<html><script type="text/javascript"> | |||
$(document).ready(function() { | $(document).ready(function() { | ||
if($('.relative-exp-of-coexp')[0]){ | if($('.relative-exp-of-coexp')[0]){ | ||
$('.relative-exp-of-coexp').DataTable({ | |||
dom: 'Blfrtip', | |||
buttons: ['copyHtml5', 'excelHtml5', 'csvHtml5', 'pdfHtml5'], | |||
lengthMenu: [[10, 50, -1], [10, 50, "All"]], | |||
order: [[ 1, 'desc' ]] | |||
}); | |||
} | |||
}); | |||
</script></html>{{#switch:{{{sample_species}}}|Human (Homo sapiens)={{#arraymap:{{#explode:{{{profile_hcage}}}|,|0}}|&|$|{{#ask:[[Coexpression_dpi_cluster_scores_median_ffid::{{PAGENAME}}]][[Coexpression_dpi_cluster_scores_median_cnhs::{{#replace:$|CNhs|}}]]|?Coexpression_dpi_cluster_scores_median_value|intro=<table class="relative-exp-of-coexp stripe cell-border order-column compact"><html><thead></html><tr><th>Coexpression cluster</th><th>score</th></tr><html></thead><tbody></html>|outro=<html></tbody></html></table>|link=none|format=template|template=Coexpression_dpi_cluster_scores_median_in_ffsample|limit=5000|searchlabel=|default=No results for this sample}} | |||
} | |||
|<br><br>}} | |<br><br>}} | ||
|Mouse (Mus musculus)= | |Mouse (Mus musculus)= | ||
{{#arraymap:{{#explode:{{{profile_hcage}}}|,|0}}|&|$ | {{#arraymap:{{#explode:{{{profile_hcage}}}|,|0}}|&|$ | ||
|<h3>$</h3 | |<h3>$</h3>{{#ask:[[Coexpression_dpi_cluster_scores_median_ffid::{{PAGENAME}}]][[Coexpression_dpi_cluster_scores_median_cnhs::{{#replace:$|CNhs|}}]]|?=MCL coexpression id|?Coexpression_dpi_cluster_scores_median_value|format=ttable|class=relative-exp-of-coexp stripe cell-border order-column compact|searchlabel=}} | ||
|<br><br> | |<br><br> | ||
}}}} | }}}} | ||
Line 177: | Line 156: | ||
repeat_enrich_byfamily_data.push([repeat_enrich_byfamily_repnames[i1],repeat_enrich_byfamily_values[i1]]); | repeat_enrich_byfamily_data.push([repeat_enrich_byfamily_repnames[i1],repeat_enrich_byfamily_values[i1]]); | ||
} | } | ||
$('#repeat_enrich_byfamily_table').DataTable({ | |||
data: repeat_enrich_byfamily_data, | |||
dom: 'Blfrtip', | |||
buttons: ['copyHtml5', 'excelHtml5', 'csvHtml5', 'pdfHtml5'], | |||
lengthMenu: [[5, 50, -1], [5, 50, "All"]], | |||
columns: [ | |||
{ title: "Repeat family" }, | |||
{ title: "Log10(Relative expression over median)" , | |||
render: function ( data, type, row, meta ) { | |||
var num = row[1]; | |||
var numb = new Number(num); | |||
return numb.toFixed(2); | |||
}}], | } | ||
} | |||
} | ], | ||
order: [[ 1, 'desc' ]] | |||
}); | |||
}); | }); | ||
</script> | </script> | ||
<span id="repeat_enrich_byfamily_table_export_tool"></span> | <span id="repeat_enrich_byfamily_table_export_tool"></span> | ||
<table id="repeat_enrich_byfamily_table"></table><br> | <table id="repeat_enrich_byfamily_table" class="stripe cell-border order-column compact"></table><br> | ||
</html> | </html> | ||
Line 216: | Line 194: | ||
<br><br>link to dataset.<br>[http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Motifs/jaspar_Significance_of_the_correlation_with_CAGE_expression data]}}<br> | <br><br>link to dataset.<br>[http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Motifs/jaspar_Significance_of_the_correlation_with_CAGE_expression data]}}<br> | ||
{{#arraymap:{{#explode:{{{profile_hcage}}}|,|0}}|&|$ | {{#arraymap:{{#explode:{{{profile_hcage}}}|,|0}}|&|$ | ||
|library id: $<span id="related_jaspar_table_export_tool"></span>{{#ask:[[jaspar_motifs_sample_pval_ffid::{{PAGENAME}}{{#replace:$|CNhs|_}}]]| | |library id: $<span id="related_jaspar_table_export_tool"></span>{{#ask:[[jaspar_motifs_sample_pval_ffid::{{PAGENAME}}{{#replace:$|CNhs|_}}]]|?=Jaspar motif|?=Logo|?jaspar_motifs_sample_pval_pval=P-value|format=ttable|limit=1100|searchlabel=|class=jaspar_motif_pval stripe cell-border order-column compact|searchlabel=|default=This sample isn't target for the analysis}} | ||
|<br> | |<br> | ||
}} | }} | ||
Line 224: | Line 202: | ||
<br><br>link to dataset.<br>[http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Motifs/novel_Significance_of_the_correlation_with_CAGE_expression data]}}<br> | <br><br>link to dataset.<br>[http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Motifs/novel_Significance_of_the_correlation_with_CAGE_expression data]}}<br> | ||
{{#arraymap:{{#explode:{{{profile_hcage}}}|,|0}}|&|$ | {{#arraymap:{{#explode:{{{profile_hcage}}}|,|0}}|&|$ | ||
|library id: $<span id="related_novel_table_export_tool"></span>{{#ask:[[novel_motifs_sample_pval_ffid::{{PAGENAME}}{{#replace:$|CNhs|_}}]]| | |library id: $<span id="related_novel_table_export_tool"></span>{{#ask:[[novel_motifs_sample_pval_ffid::{{PAGENAME}}{{#replace:$|CNhs|_}}]]|?=Novel motif|?=Logo|?novel_motifs_sample_pval_pval=P-value|format=ttable|limit=1100|searchlabel=|class=novel_motif_pval stripe cell-border order-column compact|searchlabel=|default=This sample isn't target for the analysis}} | ||
|<br> | |<br> | ||
}} | }} | ||
Line 239: | Line 217: | ||
$(document).ready(function() { | $(document).ready(function() { | ||
if($('.jaspar_motif_pval')[0]){ | if($('.jaspar_motif_pval')[0]){ | ||
$('.jaspar_motif_pval').DataTable({ | |||
dom: 'Blfrtip', | |||
buttons: ['copyHtml5', 'excelHtml5', 'csvHtml5', 'pdfHtml5'], | |||
lengthMenu: [[5, 50, -1], [5, 50, "All"]], | |||
columnDefs: [ | |||
{ targets: 0, orderable: false}, | |||
{ targets: 1, orderable: false, width: "50pt", className: "bgwhite"} | |||
], | |||
columns: [ | |||
return | { title: "Jaspar motif" }, | ||
{ title: "Logo", | |||
render: function ( data, type, row, meta ) { | |||
} | return "<img src=\"/5/sstar/seqlogo/jaspar/" + $(row[0]).text() + ".png\" width =\"80\" height = \"20\">"; | ||
} | } | ||
}, | |||
{ title: "p-value", | |||
render: function ( data, type, row, meta ) { | |||
var num=row[2]; | |||
return exp_converter(num,2,"e") ; | |||
} | |||
} | |||
], | |||
order: [[ 2, 'asc' ]] | |||
}); | |||
} | } | ||
}); | }); | ||
Line 265: | Line 251: | ||
$(document).ready(function() { | $(document).ready(function() { | ||
if($('.novel_motif_pval')[0]){ | if($('.novel_motif_pval')[0]){ | ||
$('.novel_motif_pval').DataTable({ | |||
dom: 'Blfrtip', | |||
buttons: ['copyHtml5', 'excelHtml5', 'csvHtml5', 'pdfHtml5'], | |||
lengthMenu: [[5, 50, -1], [5, 50, "All"]], | |||
columnDefs: [ | |||
{ targets: 0, orderable: false}, | |||
{ targets: 1, orderable: false, width: "50pt", className: "bgwhite"} | |||
], | |||
return | columns: [ | ||
{ title: "Novel motif" }, | |||
{ title: "Logo", | |||
} }] | render: function ( data, type, row, meta ) { | ||
return "<img src=\"/5/sstar/seqlogo/novel/" + $(row[0]).text() + ".png\" width =\"80\" height = \"20\">"; | |||
} | |||
}, | |||
{ title: "p-value", | |||
render: function ( data, type, row, meta ) { | |||
var num=row[2]; | |||
return exp_converter(num,2,"e") ; | |||
} | |||
} | |||
], | |||
order: [[ 2, 'asc' ]] | |||
}); | }); | ||
} | } | ||
}); | }); | ||
Line 293: | Line 288: | ||
</style> | </style> | ||
<script type="text/javascript" language="javascript" src="/5/sstar/rb_js/datatables/media/js/dataTables.Percentage.js"></script> | <script type="text/javascript" language="javascript" src="/5/sstar/rb_js/datatables/media/js/dataTables.Percentage.js"></script> | ||
</html> | </html> | ||
<br> | <br>|}}<!-- end of if(isHumanOrMouse) --> | ||
{{Fontsize|3|FANTOM5 (FF) ontology }} | {{Fontsize|3|FANTOM5 (FF) ontology }} | ||
---- | ---- | ||
Line 442: | Line 418: | ||
[[Category:FF_Ontology]] | [[Category:FF_Ontology]] | ||
[[Category:FF_Samples]] | [[Category:FF_Samples]] | ||
<html> | |||
<script type="text/javascript"> | |||
$(document).ready(function() { | |||
if($('.homer-table')[0]){ | |||
var homer_denovo_table = $('.homer-table').dataTable({ | |||
"bPaginate": true, | |||
"bInfo": true, | |||
"bScrollCollapse": true, | |||
"iDisplayLength": 5, | |||
"aLengthMenu": [[5,50,-1], [5,50,"All"]], | |||
"aaSorting": [], | |||
"aoColumnDefs": [{ "sType": "numeric", "sWidth": "100px", "aTargets": [2]}, {"sType": "percent", "aTargets": [ 3, 4] }, { "bSortable": false, "aTargets": [ 0, 1, 5] }] | |||
}); | |||
var homer_denovo_table_tool = new TableTools(homer_denovo_table, {"sSwfPath": "/5/sstar/rb_js/datatables/extras/TableTools/media/swf/copy_csv_xls_pdf.swf", "aButtons": [ {"sExtends": "copy", "mColumns": "visible"},{"sExtends": "csv", "mColumns": "visible"},{"sExtends": "pdf", "mColumns": "visible"} ]}); | |||
$('#homer_denovo_table_export_tool').before(homer_denovo_table_tool.dom.container ); | |||
} | |||
}); | |||
</script> | |||
</html> |
Revision as of 16:52, 23 May 2019
Name: | {{{name}}} |
---|---|
Species: | {{{sample_species}}} |
Library ID: | {{{library_id}}} |
Sample type: | {{{sample_category}}} |
Genomic View: |
Additional information | ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Sample information
RNA information
|
FANTOM5 (FF) ontology
Direct parent terms
is_a relathionship
{{{is_a}}}
part_of relathionship
{{{part_of}}}
has_quality relathionship
{{{has_quality}}}
Ancestor terms (non development)<b>Summary:</b>Connected ontology terms with is_a, part_of or located_in relationship <br><b>Analyst:</b> Hideya Kawaji<br><br>link to source data<br>data
CL: Cell type
NA
DOID: Disease
NA
UBERON: Anatomy
NA
FF: FANTOM5
NA
Ancestor terms (development)<b>Summary:</b>Connected ontology terms with develops_from, derives_from or preceded_by relationship <br><b>Analyst:</b> Hideya Kawaji <br><br>link to source data<br>data
NA