Commit 02b4bc6d authored by Mathieu Giraud's avatar Mathieu Giraud

js/scatterPlot.js: document axes

See #2060.
parent 055b45da
......@@ -115,36 +115,45 @@ function ScatterPlot(id, model, database) {
// Plot axis
this.available_axis = {
"gene_v": {
doc: "V gene (or 5' segment), gathering all alleles",
label:"V/5' gene"
},
"gene_j": {
doc: "J gene (or 3' segment), gathering all alleles",
label:"J/3' gene"
},
"allele_v": {
doc: "V gene (or 5' segment), with allele",
label:"V allele"
},
"allele_j": {
doc: "J gene (or 3' segment), with allele",
label:"J allele"
},
"sequenceLength" : {
doc: "length of the consensus sequence",
label: "clone consensus length",
fct: function(clone) {return clone.getSequenceLength()}
},
"readLength" : {
doc: "average length of the reads belonging to each clone",
label: "clone average read length",
fct: function(clone) {return clone.getAverageReadLength()}
},
"GCContent" : {
doc: "%GC content of the consensus sequence of each clone",
label: "GC content",
fct: "GCContent",
output: "percent"
},
"n": {
doc: "N length, from the end of the V/5' segment to the start of the J/3' segment (excluded)",
label: "N length",
fct: function(clone) {return clone.getNlength()}
},
"lengthCDR3": {
label: "CDR3 length",
doc: "CDR3 length, in nucleotides, from Cys104 and Phe118/Trp118 (excluded)",
label: "CDR3 length (nt)",
fct: function(clone) {return clone.getSegLength('cdr3')}
},
"productivity": {
......@@ -153,11 +162,14 @@ function ScatterPlot(id, model, database) {
output: "string-sorted"
},
"tag": {
doc: "tag, as defined by the user",
label: "tag",
fct: function(clone) {return clone.getTagName()},
output: "string-sorted"
},
"coverage": {
doc: "ratio of the length of the clone consensus sequence to the median read length of the clone",
// "Coverage between .85 and 1.0 (or more) are good values",
label: "clone consensus coverage",
fct: function(clone){return clone.coverage},
min: 0,
......@@ -166,11 +178,13 @@ function ScatterPlot(id, model, database) {
log: false
},
"locus" : {
doc: "locus or recombination system",
label: "locus",
fct: function(clone){return clone.germline},
output: "string-sorted"
},
"Size" : {
doc: "ratio of the number of reads of each clone to the total number of reads in the selected locus",
label: "size",
fct : function(clone){return clone.getSizeZero()},
min : function(){return self.m.min_size},
......@@ -179,7 +193,8 @@ function ScatterPlot(id, model, database) {
log : true
},
"otherSize" : {
label: "size (other point)",
doc: "ratio of the number of reads of each clone to the total number of reads in the selected locus, on a second sample",
label: "size (other sample)",
fct : function(clone){return clone.getSizeZero(m.tOther)},
min : function(){return self.m.min_size},
max : 1,
......
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