Commit 52998016 authored by Mathieu Giraud's avatar Mathieu Giraud

js/axes.js, js/scatterPlot.js: bikeshedding axes names

See #2781.
parent b4f7e5fd
......@@ -59,14 +59,14 @@ Axes.prototype = {
label:"J allele",
axis: new GermlineAxis(this.m, false, true)
},
"sequenceLength" : {
"consensusLength" : {
doc: "length of the consensus sequence",
label: "clone consensus length",
axis: new NumericalAxis(this.m, false, false),
fct: function(clone) {return clone.getSequenceLength()},
pretty: function(len) { return createClassedSpan('threeDigits', len) }
},
"readLength" : {
"averageLength" : {
doc: "average length of the reads belonging to each clone",
label: "clone average read length",
axis: new FloatAxis(this.m),
......@@ -79,7 +79,7 @@ Axes.prototype = {
axis: new PercentAxis(this.m),
fct: "GCContent"
},
"n": {
"nLength": {
doc: "N length, from the end of the V/5' segment to the start of the J/3' segment (excluded)",
label: "N length",
axis: new NumericalAxis(this.m),
......@@ -106,7 +106,7 @@ Axes.prototype = {
pretty: function(tag) { return icon_pm(tag, "productive", "not productive") },
hide: true
},
"VIdentity-IMGT": {
"vIdentity-IMGT": {
label: "V identity (as computed by IMGT/V-QUEST)",
axis: new NumericalAxis(this.m),
fct: function(clone) { return clone.getVIdentityIMGT() },
......@@ -152,7 +152,7 @@ Axes.prototype = {
pretty: function(system) { return self.m.systemBox(system) },
sort: true
},
"Size" : {
"size" : {
doc: "ratio of the number of reads of each clone to the total number of reads in the selected locus",
label: "size",
axis: new PercentAxis(this.m),
......@@ -162,7 +162,7 @@ Axes.prototype = {
max : 1,
log : true
},
"otherSize" : {
"sizeOtherSample" : {
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)",
axis: new PercentAxis(this.m),
......@@ -250,13 +250,13 @@ Axes.prototype = {
label: "interpolated length, between BIOMED2 primers (inclusive)",
fct: function(cloneID) {return self.m.clone(cloneID).getSegLengthDoubleFeature('primer5', 'primer3')}
},
"delRight": {
"vDel": {
doc: "number of deleted nucleotides at the 3' side of the V/5' segment",
label: "V/5' deletions in 3'",
axis: new NumericalAxis(this.m),
fct: function(clone) { return clone.getDeletion('5', 'delRight') }
},
"delLeft": {
"jDel": {
doc: "number of deleted nucleotides at the 5' side of the J/3' segment",
label: "J/3' deletions in 5'",
axis: new NumericalAxis(this.m),
......
......@@ -128,23 +128,23 @@ function ScatterPlot(id, model, database) {
this.preset = {
"V/J (genes)" : { "mode": this.MODE_GRID, "x" : this.AXIS_GENE_V, "y": this.AXIS_GENE_J},
"V/J (alleles)" : { "mode": this.MODE_GRID, "x" : this.AXIS_ALLELE_V, "y": this.AXIS_ALLELE_J},
"V/N length" : { "mode": this.MODE_GRID, "x" : this.AXIS_GENE_V, "y": "n"},
"clone consensus length / locus" : { "mode": this.MODE_GRID, "x": "sequenceLength", "y" : "locus"},
// "V/abundance" : { "mode": this.MODE_GRID, "x" : this.AXIS_GENE_V, "y": "Size"},
"clone consensus length distribution" : { "mode": this.MODE_BAR, "x" : "sequenceLength", "y": "Size"},
"V distribution" : { "mode": this.MODE_BAR, "x" : this.AXIS_GENE_V, "y": "Size"},
"N length distribution" : { "mode": this.MODE_BAR, "x" : "n", "y": this.AXIS_GENE_V},
"CDR3 length distribution" : { "mode": this.MODE_BAR, "x": "lengthCDR3", "y" : "Size"},
"J distribution" : { "mode": this.MODE_BAR, "x" : this.AXIS_GENE_J, "y": "Size"},
"compare two samples" : { "mode": this.MODE_GRID, "x" : "Size", "y": "otherSize"},
"V/N length" : { "mode": this.MODE_GRID, "x" : this.AXIS_GENE_V, "y": "nLength"},
"clone consensus length / locus" : { "mode": this.MODE_GRID, "x": "consensusLength", "y" : "locus"},
// "V/abundance" : { "mode": this.MODE_GRID, "x" : this.AXIS_GENE_V, "y": "size"},
"clone consensus length distribution" : { "mode": this.MODE_BAR, "x" : "consensusLength", "y": "size"},
"V distribution" : { "mode": this.MODE_BAR, "x" : this.AXIS_GENE_V, "y": "size"},
"N length distribution" : { "mode": this.MODE_BAR, "x" : "nLength", "y": this.AXIS_GENE_V},
"CDR3 length distribution" : { "mode": this.MODE_BAR, "x": "lengthCDR3", "y" : "size"},
"J distribution" : { "mode": this.MODE_BAR, "x" : this.AXIS_GENE_J, "y": "size"},
"compare two samples" : { "mode": this.MODE_GRID, "x" : "size", "y": "sizeOtherSample"},
"plot by similarity" : { "mode": this.MODE_GRID, "x" : "tsneX", "y": "tsneY"},
"plot by similarity and by locus" : { "mode": this.MODE_GRID, "x" : "tsneX_system", "y": "tsneY_system"},
"clone consensus length / GC content " : { "mode": this.MODE_GRID, "x": "sequenceLength", "y" : "GCContent"},
"clone consensus length / GC content " : { "mode": this.MODE_GRID, "x": "consensusLength", "y" : "GCContent"},
"clone consensus coverage / GC content " : { "mode": this.MODE_GRID, "x": "coverage", "y" : "GCContent"},
"number of samples sharing each clone" : { "mode": this.MODE_GRID, "x": "nbSamples", "y" : "locus"},
// "interpolated length between BIOMED2 primers (inclusive)" : { "mode": this.MODE_BAR, "x": "primers", "y" : "Size"},
"number of deletions for the segment V/5 in 3" : { "mode": this.MODE_BAR, "x": "delRight", "y" : "Size"},
"number of deletions for the segment J/3 in 5" : { "mode": this.MODE_BAR, "x": "delLeft", "y" : "Size"},
// "interpolated length between BIOMED2 primers (inclusive)" : { "mode": this.MODE_BAR, "x": "primers", "y" : "size"},
"number of deletions for the segment V/5 in 3" : { "mode": this.MODE_BAR, "x": "vDel", "y" : "size"},
"number of deletions for the segment J/3 in 5" : { "mode": this.MODE_BAR, "x": "jDel", "y" : "size"},
};
this.default_preset = 1
......
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