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Fixed issue with relative RPKM
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Bug fix:
• Fixed issue where relative RPKM would not display the correct information
• If a sample has no control data, now uses the median of all samples instead of empty data
• Added gene variant information (GFF) to the compare gene variants option
• Removed 'Show More Details' from compare gene variants which were causing certain bugs with the table information
• To prevent issues with compare gene variants, if on relative mode, disabled compare gene variants
• Fixed an issue relating to table toggle and compare gene variants

TODO:
• Make eFP Overview more responsive to the screen's resolution
• TMM or TPM and median for additional normalization methods
• Expand the creation of the private database to include adding from public and private database to your creation

Known bugs:
• Does not work on IE
• Google Drive repos do not work for IGB links
• Download page as an image does not render SVGs on Microsoft Edge
• Some sorting arrows may not display in Microsoft Edge
  • Loading branch information
@AlexJSully
AlexJSully committed Jun 25, 2019
1 parent 1f5150d commit cc1f498
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Showing 5 changed files with 101 additions and 49 deletions.
121 changes: 81 additions & 40 deletions cgi-bin/core/custom.js
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Original file line number Diff line number Diff line change
Expand Up @@ -332,6 +332,26 @@ function colour_part_by_id(id, part, fpkm, mode) {
};
};

var rpkmAverage = 1; // Set to 1 as default so prevents the divide by 0 zero later
var rpkmMedian = 1; // Set to 1 as default so prevents the divide by 0 zero later
/**
* Find the RPKM average across all samples
*/
function findRPKMValuesAcrossAll() {
var listOfSRA = Object.keys(sraDict);
var listOfRPKM = [];
var rpkmTotal = 0;
for (var l = 0; l < listOfSRA.length; l++) {
if (sraDict[listOfSRA[l]]["RPKM"]) {
var currentRPKM = sraDict[listOfSRA[l]]["RPKM"][variantPosition];
listOfRPKM.push(currentRPKM);
rpkmTotal += currentRPKM;
};
};
rpkmMedian = math.median(rpkmMedian);
rpkmAverage = (rpkmTotal / listOfSRA.length);
};

var current_radio = "abs";
/**
* Find and update each SVG in the DOM.
Expand All @@ -341,6 +361,7 @@ function colour_svgs_now(mode) {
mode = colouring_mode;
current_radio = $('input[type="radio"][name="svg_colour_radio_group"]:checked').val();
for (var i = 0; i < count_bam_entries_in_xml; i++) {
var currentSRA = exp_info[i][0].slice(0, -4);
// For every exp, figure out the fpkm average of the controls
var ctrl_fpkm_sum = 0;
var ctrl_count = 0;
Expand All @@ -349,36 +370,46 @@ function colour_svgs_now(mode) {
if (exp_info[i][2].indexOf(exp_info[ii][0].slice(0, -4)) != -1) {
// experiment ii is a control for experiment i, save FPKM of exp ii
ctrl_count++;
ctrl_fpkm_sum += exp_info[ii][3];
ctrl_fpkm_sum += exp_info[ii][3][variantPosition];
};
};
// If no control found:
if (ctrl_fpkm_sum === 0 && sraDict[currentSRA]['RPKM']) {
ctrl_fpkm_sum = sraDict[currentSRA]['RPKM'][variantPosition];
};

// Create control average
if (ctrl_count > 0) {
ctrl_avg_fpkm = ctrl_fpkm_sum / ctrl_count;
} else {
if (rpkmMedian === 1) {
findRPKMValuesAcrossAll();
};
ctrl_avg_fpkm = rpkmMedian;
};

// Save the average fpkm of controls and the log fpkm...
var relativeRPKMValue = 0;
var relativeRPKM = [];
if (ctrl_count > 0) {
for (var v = 0; v < exp_info[0][3].length; v++) {
if (exp_info[i][3][variantPosition] == 0 && ctrl_avg_fpkm == 0) {
if (sraDict[currentSRA]['RPKM'][variantPosition] == 0 && ctrl_avg_fpkm == 0) {
// Define log2(0/0) = 0 as opposed to undefined
// Define log2(0/0) = 0 as opposed to undefined
relativeRPKM.push(0);
exp_info[i].splice(4, 1, 0);
} else {
relativeRPKM.push(Math.log2(exp_info[i][3][variantPosition] / ctrl_avg_fpkm))
};
};
// Define log2(0/0) = 0 as opposed to undefined
relativeRPKMValue = 0;
exp_info[i].splice(4, 1, 0);
} else {
for (var v = 0; v < exp_info[0][3].length; v++) {
relativeRPKM.push("Missing controls data");
};
relativeRPKMValue = (Math.log2(sraDict[currentSRA]['RPKM'][variantPosition] / ctrl_avg_fpkm));
};
relativeRPKM.push(relativeRPKMValue);
sraDict[currentSRA]['relativeRPKM'] = relativeRPKMValue;

exp_info[i].splice(4, 1, relativeRPKM);
exp_info[i].splice(6, 1, ctrl_avg_fpkm);

// See if the absolute or the relative FPKM is max
if (exp_info[i][3][variantPosition] >= max_absolute_fpkm) {
max_absolute_fpkm = exp_info[i][3][variantPosition];
if (sraDict[currentSRA]['RPKM'][variantPosition] >= max_absolute_fpkm) {
max_absolute_fpkm = sraDict[currentSRA]['RPKM'][variantPosition];
document.getElementById("rpkm_scale_input").value = parseInt(round(max_absolute_fpkm));
};
if (exp_info[i][4] != "Missing controls data" && Math.abs(exp_info[i][4]) >= max_log_fpkm && Math.abs(exp_info[i][4]) < 1000) {
max_log_fpkm = Math.abs(exp_info[i][4]);
Expand All @@ -389,13 +420,12 @@ function colour_svgs_now(mode) {
if (!exp_info[i][4] && exp_info[i][4] != 0) {
exp_info[i][4] = -999999;
};
colour_part_by_id(exp_info[i][0], exp_info[i][1], exp_info[i][4], colouring_mode); // index 5 = relative fpkm
} else {
if (!exp_info[i][3][variantPosition] && exp_info[i][3][variantPosition] != 0) {
exp_info[i][3][variantPosition] = -999999;
};
colour_part_by_id(exp_info[i][0], exp_info[i][1], exp_info[i][3], colouring_mode); // index 3 = absolute fpkm
};
whichAbsOrRel();
};

$("#theTable").trigger("update");
Expand Down Expand Up @@ -566,23 +596,28 @@ function whichAbsOrRel(preIterate = false, iteratePos = 0) {
*/
function absOrRel(expInfoPos = 0) {
var expInfo = exp_info[expInfoPos];
var currentSRA = expInfo[0].slice(0, -4);
// Update RPKM values and colours
if (colouring_mode == "rel") {
if (colouring_mode == "rel" && sraDict[currentSRA]['relativeRPKM']) {
document.getElementById('compareGeneVariants').disabled = true;
if (!expInfo[4] && expInfo[4] != 0) {
expInfo[4] = -999999;
};
var rpkmValue = expInfo[5][variant_selected].toFixed(2);
var rpkmValue = sraDict[currentSRA]['relativeRPKM'].toFixed(2);
document.getElementById(expInfo[0].split("_svg")[0] + '_rpkm').innerHTML = rpkmValue;
sraDict[expInfo[0].split("_svg")[0]]["rpkm"] = rpkmValue;
colour_part_by_id(expInfo[0], expInfo[1], expInfo[5], colouring_mode); // index 5 = relative fpkm
colour_part_by_id(currentSRA + '_svg', sraDict[currentSRA]['svg_part'], sraDict[currentSRA]['relativeRPKM'], colouring_mode); // index 5 = relative fpkm
} else {
if (allCheckedOptions.length > 0) {
document.getElementById('compareGeneVariants').disabled = false;
}
if (!expInfo[3] && expInfo[3] != 0) {
expInfo[3] = -999999;
};
var rpkmValue = expInfo[3][variant_selected].toFixed(2);
var rpkmValue = sraDict[currentSRA]['RPKM'][variant_selected].toFixed(2);
document.getElementById(expInfo[0].split("_svg")[0] + '_rpkm').innerHTML = rpkmValue;
sraDict[expInfo[0].split("_svg")[0]]["rpkm"] = rpkmValue;
colour_part_by_id(expInfo[0], expInfo[1], expInfo[3], colouring_mode); // index 3 = absolute fpkm
colour_part_by_id(currentSRA + '_svg', sraDict[currentSRA]['svg_part'], sraDict[currentSRA]['RPKM'][variant_selected], colouring_mode); // index 3 = absolute fpkm
};
};

Expand All @@ -605,6 +640,7 @@ var totalreadsMapped_dic = {};
var dumpOutputs = "";
var dumpMethod = "simple";
var callDumpOutputs = false;
var rpkmCount = 1;
/**
* Makes AJAX request for each RNA-Seq image based on the rnaseq_calls array that was produced by the populate_table() function
*/
Expand All @@ -620,6 +656,7 @@ function rnaseq_images(status) {
dumpOutputs = "";
data = {};
rnaseq_success = 1;
rpkmCount = 1;
match_drive = "";
// Start
get_input_values();
Expand Down Expand Up @@ -726,6 +763,7 @@ function rnaseq_images(status) {
sraDict[response_rnaseq['record']]["rpb"] = parseFloat(r[0]).toFixed(2);
document.getElementById(response_rnaseq['record'] + '_rpkm').innerHTML = response_rnaseq['absolute-fpkm'];
sraDict[response_rnaseq['record']]["RPKM"] = response_rnaseq['absolute-fpkm'];
rpkmCount++;
document.getElementById(response_rnaseq['record'] + '_totalReadsNum').innerHTML = "Total reads = " + response_rnaseq['totalReadsMapped'];

// Generate pre-caching information
Expand Down Expand Up @@ -764,21 +802,16 @@ function rnaseq_images(status) {

colour_part_by_id(response_rnaseq['record'] + '_svg', 'Shapes', response_rnaseq['absolute-fpkm'][variantPosition], colouring_mode);

if (rnaseq_success == count_bam_entries_in_xml || rnaseq_success % 10 == 0) {
// Execute the colour_svgs_now() function
colour_svgs_now();
// Change the input box value to max absolute fpkm
document.getElementById("rpkm_scale_input").value = parseInt(round(max_absolute_fpkm));
// Execute the colour_svgs_now() function and use the new max absolute fpkm
colour_svgs_now();
if (rnaseq_success == count_bam_entries_in_xml) {
if (rpkmCount == count_bam_entries_in_xml) {
setTimeout(function(){
colour_svgs_now();
date_obj4 = new Date();
rnaseq_success_end_time = date_obj4.getTime(); // Keep track of start time
//console.log(rnaseq_success_end_time);
document.getElementById('progress_tooltip').innerHTML = rnaseq_success + " / count_bam_entries_in_xml requests completed<br/>Load time ~= " + String(round(parseInt(rnaseq_success_end_time - rnaseq_success_start_time) / (1000 * 60))) + " mins.";
//console.log("**** Requests = " + String(rnaseq_success) + ", time delta = " + String(parseInt(rnaseq_success_end_time - rnaseq_success_start_time)));
};
};
}, 100);
};

$("#theTable").trigger("update");
responsiveRNAWidthResize();
Expand Down Expand Up @@ -1062,6 +1095,8 @@ function populate_table(status) {
sraDict = {};
sraCountDic = {};
tissueSRADic = {};
rpkmAverage = 1;
rpkmMedian = 1;

// Creating exon intron scale image
var img_created = '<img src="' + 'data:image/png;base64,' + exon_intron_scale + '" alt="RNA-Seq mapped image" style="float: right; margin-right: 10px;">';
Expand All @@ -1075,7 +1110,7 @@ function populate_table(status) {
'<th class="coleFP" id="eFP_th" class="sortable" style="border: 1px solid #D3D3D3; background-color: #F0F0F0; width: 100px;">eFP (RPKM)</th>' +
'<th class="sortable colRPKM" id="colRPKM" onclick="ChangeColArrow(this.id)" title="Reads Per Kilobase of transcript per Million mapped reads. Higher number suggest more mapped reads/expression" style="border: 1px solid #D3D3D3; background-color: #F0F0F0; width: 75px;"><div class="row" id="colRPKMRow"><div class="col-xs-7">RPKM</div><div class="col-xs-1"><img class="sortingArrow" id="colRPKMArrow" src="./cgi-bin/SVGs/arrowDefault.min.svg"></div></div></th>' +
'<th class="sortable colDetails" id="colDetails" onclick="ChangeColArrow(this.id)" style="border: 1px solid #D3D3D3; background-color: #F0F0F0; width: 275px;"><div class="row" id="colDetailsRow"><div class="col-xs-10">Details</div><div class="col-xs-0.5"><img class="sortingArrow" id="colDetailsArrow" src="./cgi-bin/SVGs/arrowDefault.min.svg"></div></div></th>' +
'<th class="sortable colCompare" id="colCompare" style="border: 1px solid #D3D3D3; background-color: #F0F0F0; max-width: 30px;"><div class="row" id="colCompareRow"></div></th>' +
'<th class="sortable colCompare" id="colCompare" style="border: 1px solid #D3D3D3; background-color: #F0F0F0; max-width: 30px;" hidden><div class="row" id="colCompareRow"></div></th>' +
'</tr></thead>' +
'<tbody id="data_table_body"></tbody>';
$("#theTable").append(tableHeader);
Expand Down Expand Up @@ -1491,9 +1526,9 @@ function populate_efp_modal(status) {

// Check radio
if (current_radio == "abs") {
$("#efpModalTable").append('<p class="eFP_thead"> eFP Colour Scale: <img src="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAGQAAAAPCAMAAAAlD5r/AAABQVBMVEX///8AAADcFDz/jAAAAP+m 3KYAfQD//wD//AD/+QD/9wD/9AD/8gD/7wD/7QD/6gD/6AD/5QD/4gD/4AD/3QD/2wD/2AD/1gD/ 0wD/0QD/zgD/zAD/yQD/xgD/xAD/wQD/vwD/vAD/ugD/twD/tQD/sgD/rwD/rQD/qgD/qAD/pQD/ owD/oAD/ngD/mwD/mQD/lgD/kwD/kQD/jgD/jAD/iQD/hwD/hAD/ggD/fwD/fAD/egD/dwD/dQD/ cgD/cAD/bQD/awD/aAD/ZgD/YwD/YAD/XgD/WwD/WQD/VgD/VAD/UQD/TwD/TAD/SQD/RwD/RAD/ QgD/PwD/PQD/OgD/OAD/NQD/MwD/MAD/LQD/KwD/KAD/JgD/IwD/IQD/HgD/HAD/GQD/FgD/FAD/ EQD/DwD/DAD/CgD/BwD/BQD/AgCkIVxRAAAAs0lEQVQ4jWNg5+Dk4ubh5eMXEBQSFhEVE5eQlJKW kZWTV1BUUlZRVVPX0NTS1tHV0zcwNDI2MTUzt7C0sraxtbN3cHRydnF1c/fw9PL28fXzDwgMCg4J DQuPiIyKjomNi09ITEpOSU1Lz8jMYhi1hERLGBmpbgljbBwjiiWMnFyMVLcECOhkCZBIZUzPYKSV JaDgYkxKZkxNY2SkmU8gljDCLaFdxDMmw4NrGOWTUUuItwQAG8496iMoCNwAAAAASUVORK5CYII=" alt="Absolute RPKM"> Min: ' + Math.min.apply(null, efp_RPKM_values).toFixed(1) + ' RPKM, Max: ' + Math.max.apply(null, efp_RPKM_values).toFixed(1) + ' RPKM</p>' + '<br><table><tbody class="eFP_tbody"></tbody>');
$("#efpModalTable").append('<p class="eFP_thead"> eFP Colour Scale: <img src="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAGQAAAAPCAMAAAAlD5r/AAABQVBMVEX///8AAADcFDz/jAAAAP+m 3KYAfQD//wD//AD/+QD/9wD/9AD/8gD/7wD/7QD/6gD/6AD/5QD/4gD/4AD/3QD/2wD/2AD/1gD/ 0wD/0QD/zgD/zAD/yQD/xgD/xAD/wQD/vwD/vAD/ugD/twD/tQD/sgD/rwD/rQD/qgD/qAD/pQD/ owD/oAD/ngD/mwD/mQD/lgD/kwD/kQD/jgD/jAD/iQD/hwD/hAD/ggD/fwD/fAD/egD/dwD/dQD/ cgD/cAD/bQD/awD/aAD/ZgD/YwD/YAD/XgD/WwD/WQD/VgD/VAD/UQD/TwD/TAD/SQD/RwD/RAD/ QgD/PwD/PQD/OgD/OAD/NQD/MwD/MAD/LQD/KwD/KAD/JgD/IwD/IQD/HgD/HAD/GQD/FgD/FAD/ EQD/DwD/DAD/CgD/BwD/BQD/AgCkIVxRAAAAs0lEQVQ4jWNg5+Dk4ubh5eMXEBQSFhEVE5eQlJKW kZWTV1BUUlZRVVPX0NTS1tHV0zcwNDI2MTUzt7C0sraxtbN3cHRydnF1c/fw9PL28fXzDwgMCg4J DQuPiIyKjomNi09ITEpOSU1Lz8jMYhi1hERLGBmpbgljbBwjiiWMnFyMVLcECOhkCZBIZUzPYKSV JaDgYkxKZkxNY2SkmU8gljDCLaFdxDMmw4NrGOWTUUuItwQAG8496iMoCNwAAAAASUVORK5CYII=" alt="Absolute RPKM" class="colourScale"> Min: ' + Math.min.apply(null, efp_RPKM_values).toFixed(1) + ' RPKM, Max: ' + Math.max.apply(null, efp_RPKM_values).toFixed(1) + ' RPKM</p>' + '<br><table><tbody class="eFP_tbody"></tbody>');
} else if (current_radio == "rel") {
$("#efpModalTable").append('<p class="eFP_thead"> eFP Colour Scale: <img src="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAGQAAAAPCAMAAAAlD5r/AAABQVBMVEX///8AAADcFDz/jAAAAP+m 3KYAfQAAAP8FBfkKCvQPD+8UFOoZGeUeHuAjI9soKNYtLdEzM8w4OMY9PcFCQrxHR7dMTLJRUa1W VqhbW6NgYJ5mZplra5NwcI51dYl6eoR/f3+EhHqJiXWOjnCTk2uZmWaenmCjo1uoqFatrVGysky3 t0e8vELBwT3GxjjMzDPR0S3W1ijb2yPg4B7l5Rnq6hTv7w/09Ar5+QX//wD/+wD/9gD/8QD/7AD/ 5wD/4gD/3QD/2AD/0wD/zQD/yAD/wwD/vgD/uQD/tAD/rwD/qgD/pQD/oAD/mgD/lQD/kAD/iwD/ hgD/gQD/fAD/dwD/cgD/bQD/ZwD/YgD/XQD/WAD/UwD/TgD/SQD/RAD/PwD/OgD/NAD/LwD/KgD/ JQD/IAD/GwD/FgD/EQD/DAD/BwBUljDTAAAA1klEQVQ4jWNg5+Dk4ubh5eMXEBQSFhEVE5eQlJKW kZWTV1BUUlZRVVPX0NTS1tHV0zcwNDI2MTUzt7C0sraxtbN3cHRydnF1c/fw9PL28fXzDwgMCg4J DQuPiIyKjomNi09ITEpOSU1Lz8jMYhi1hDRLGDi5GICWMBBvCSMjIUsYY+MYUS0BApJ8wmhlzUjI EiDAYgkD0CcMwgxUtQRIpDKmZzCiBBcDgwgDlSwBBRdjUjJjahojI2qcMAhT2RJGNEuAYUasJURH PGMyPLiGTz4ZtYQESwCEoDnh8dGTkQAAAABJRU5ErkJggg==" alt="Relative RPKM"> Min: ' + Math.min.apply(null, efp_RPKM_values).toFixed(1) + ', Max: ' + Math.max.apply(null, efp_RPKM_values).toFixed(1) + '</p>' + '<br><table><tbody></tbody>');
$("#efpModalTable").append('<p class="eFP_thead"> eFP Colour Scale: <img src="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAGQAAAAPCAMAAAAlD5r/AAABQVBMVEX///8AAADcFDz/jAAAAP+m 3KYAfQAAAP8FBfkKCvQPD+8UFOoZGeUeHuAjI9soKNYtLdEzM8w4OMY9PcFCQrxHR7dMTLJRUa1W VqhbW6NgYJ5mZplra5NwcI51dYl6eoR/f3+EhHqJiXWOjnCTk2uZmWaenmCjo1uoqFatrVGysky3 t0e8vELBwT3GxjjMzDPR0S3W1ijb2yPg4B7l5Rnq6hTv7w/09Ar5+QX//wD/+wD/9gD/8QD/7AD/ 5wD/4gD/3QD/2AD/0wD/zQD/yAD/wwD/vgD/uQD/tAD/rwD/qgD/pQD/oAD/mgD/lQD/kAD/iwD/ hgD/gQD/fAD/dwD/cgD/bQD/ZwD/YgD/XQD/WAD/UwD/TgD/SQD/RAD/PwD/OgD/NAD/LwD/KgD/ JQD/IAD/GwD/FgD/EQD/DAD/BwBUljDTAAAA1klEQVQ4jWNg5+Dk4ubh5eMXEBQSFhEVE5eQlJKW kZWTV1BUUlZRVVPX0NTS1tHV0zcwNDI2MTUzt7C0sraxtbN3cHRydnF1c/fw9PL28fXzDwgMCg4J DQuPiIyKjomNi09ITEpOSU1Lz8jMYhi1hDRLGDi5GICWMBBvCSMjIUsYY+MYUS0BApJ8wmhlzUjI EiDAYgkD0CcMwgxUtQRIpDKmZzCiBBcDgwgDlSwBBRdjUjJjahojI2qcMAhT2RJGNEuAYUasJURH PGMyPLiGTz4ZtYQESwCEoDnh8dGTkQAAAABJRU5ErkJggg==" alt="Relative RPKM" class="colourScale"> Min: ' + Math.min.apply(null, efp_RPKM_values).toFixed(1) + ', Max: ' + Math.max.apply(null, efp_RPKM_values).toFixed(1) + '</p>' + '<br><table><tbody></tbody>');
};

// Insert eFP Table
Expand Down Expand Up @@ -2458,6 +2493,7 @@ function toggleResponsiveTableOptions(colTitleBool, colRNABool, colrpbBool, cole
document.getElementById("toggleDetails").checked = colDetailsBool;
toggleTableCol("colCompare", colCompareBool);
document.getElementById("toggleCompare").checked = colCompareBool;

RememberToggleOptions(colTitleBool, colRNABool, colrpbBool, coleFPBool, colRPKMBool, colDetailsBool, colCompareBool);
};

Expand Down Expand Up @@ -2490,7 +2526,7 @@ function toggleResponsiveTable(forceToggle = 0, buttonClick = false) {
};
};

var ToggledTable = [true, true, true, true, true, true];
var ToggledTable = [true, true, true, true, true, true, false];
/**
* Remember what toggle options were chosen in the RNA table
* @param {boolean} [title=true] Title
Expand Down Expand Up @@ -2756,6 +2792,7 @@ function generateShareLink() {
document.getElementById('shareLinkTextArea').innerHTML = shareLink;
};

var shareLinkInputs = {};
/**
* Read shared link and display data if appropriate
*/
Expand All @@ -2777,10 +2814,12 @@ function readShareLink() {
// If locus
if (queryInputs[0] === 'locus') {
var qIValue = inputs[i].substr(6);
shareLinkInputs['locus'] = qIValue;
document.getElementById('locus').value = qIValue;
locusInput = true;
} else if (queryInputs[0] === 'dataset') {
var qIValue = inputs[i].substr(8);
shareLinkInputs['dataset'] = qIValue;
base_src = qIValue;
datasetInput = true;
};
Expand Down Expand Up @@ -2836,9 +2875,9 @@ function tableCheckbox(whatID, disableAll = false) {
var append_str = '<tr class="compareDataRow" id="' + whatSRA + '_compareRow' + i + '">';
// Append title <td>
if (parseInt(i) === parseInt(variantPosition)) {
append_str += '<td style="width: 250px; font-size: 12px;" id="' + whatSRA + '_compareTitle' + i + '">' + document.getElementById(whatSRA + '_title').innerHTML + '</td>\n';
append_str += '<td style="width: 250px; font-size: 12px;" id="' + whatSRA + '_compareTitle' + i + '">' + document.getElementById(whatSRA + '_title').innerHTML + ' ... (' + GFF_List[i] + ')</td>\n';
} else {
append_str += '<td style="width: 250px; font-size: 12px;" id="' + whatSRA + '_compareTitle' + i + '">^^^</td>\n';
append_str += '<td style="width: 250px; font-size: 12px;" id="' + whatSRA + '_compareTitle' + i + '">^^^ ... (' + GFF_List[i] + ')</td>\n';
};
// Append RNA-Seq and Gene Structure images (2 imgs) in one <td>
append_str += '<td style="max-width: 576px;">' + '<img id="' + whatSRA + '_rnaseq_img' + i + '" alt="RNA-Seq mapped image for:' + whatSRA + '" style="min-width:420px; max-width:576px; width:95%; height: auto;" src="" /><br/>' + '<img id="' + whatSRA + '_gene_structure_img' + i + '" style="max-width: 576px; width:100%; height: auto;" src="" alt="Gene variant image for:' + whatSRA + '"/>' + '</td>\n';
Expand All @@ -2850,7 +2889,7 @@ function tableCheckbox(whatID, disableAll = false) {
append_str += '<td id="' + whatSRA + '_rpkm' + i + '" style="font-size: 12px; width: 50px; ">' + sraDict[whatSRA]["RPKM"][i].toFixed(2) + '</td>';
// Append the details <td>
if (parseInt(i) === parseInt(variantPosition)) {
append_str += '<td style="width: 250px; font-size: 12px;" id="' + whatSRA + '_compareTitle' + i + '">' + document.getElementById(whatSRA + '_details').innerHTML + '</td>\n';
append_str += '<td style="width: 250px; font-size: 12px;" id="' + whatSRA + '_compareTitle' + i + '"><div id="' + whatSRA + '_descriptionCompare" name="' + document.getElementById(whatSRA + '_description').getAttribute('name') + '">' + document.getElementById(whatSRA + '_description').innerHTML + '</div><div id="igbLinkCompare_' + whatSRA + '">' + document.getElementById('igbLink_' + whatSRA).innerHTML + '</div><div id="extraLinksCompare_' + whatSRA + '">' + document.getElementById('extraLinks_' + whatSRA).innerHTML + '</div></td>\n';
} else {
append_str += '<td style="width: 250px; font-size: 12px;" id="' + whatSRA + '_compareTitle' + i + '">^^^</td>\n';
};
Expand All @@ -2870,7 +2909,9 @@ function tableCheckbox(whatID, disableAll = false) {
};
document.getElementById(whatID).checked = true;
document.getElementById('allCheckbox').checked = true;
document.getElementById('compareGeneVariants').disabled = false;
if (colouring_mode != 'rel') {
document.getElementById('compareGeneVariants').disabled = false;
};
} else {
// If unchecked, remove compare entries
if (disableAll === false) {
Expand Down
3 changes: 2 additions & 1 deletion cgi-bin/core/custom.min.js
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4 changes: 4 additions & 0 deletions cgi-bin/core/style.css
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Original file line number Diff line number Diff line change
Expand Up @@ -615,4 +615,8 @@ li > p {
.colCompare {
vertical-align: middle !important;
text-align: center;
}

.colourScale {
max-width: 100px;
}
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