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evanbiederstedtevanbiederstedt
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fix html
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‎CHANGELOG.md

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## Upcoming
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## [1.0.7] - 2020-11-14
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- Added ability to export data in grids as *csv
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- Small revisions to docs
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## [1.0.6] - 2020-10-06
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- Fixed `read10xMatrix()` to work with new 10x files

‎DESCRIPTION

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Package: pagoda2
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Title: Single Cell Analysis and Differential Expression
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Version: 1.0.6
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Version: 1.0.7
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Authors@R: c(person("Nikolas","Barkas", email="[email protected]", role="aut"), person("Viktor", "Petukhov", email="[email protected]", role="aut"), person("Peter", "Kharchenko", email = "[email protected]", role = "aut"), person("Simon", "Steiger", email = "[email protected]", role = "ctb"), person("Evan", "Biederstedt", email="[email protected]", role=c("cre", "aut")))
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Description: Analyzing and interactively exploring large-scale single-cell RNA-seq datasets. 'pagoda2' primarily performs normalization and differential gene expression analysis, with an interactive application for exploring single-cell RNA-seq datasets. It performs basic tasks such as cell size normalization, gene variance normalization, and can be used to identify subpopulations and run differential expression within individual samples. 'pagoda2' was written to rapidly process modern large-scale scRNAseq datasets of approximately 1e6 cells. The companion web application allows users to explore which gene expression patterns form the different subpopulations within your data. The package also serves as the primary method for preprocessing data for conos, <https://github.com/kharchenkolab/conos>. This package interacts with data available through the 'p2data' package, which is available in a 'drat' repository. To access this data package, see the instructions at <https://github.com/kharchenkolab/pagoda2>. The size of the 'p2data' package is approximately 6 MB.
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License: GPL-3

‎README.md

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```
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Nikolas Barkas, Viktor Petukhov, Peter Kharchenko and Evan
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Biederstedt (2021). pagoda2: Single Cell Analysis and Differential
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Expression. R package version 1.0.6.
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Expression. R package version 1.0.7.
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```

‎doc/pagoda2.walkthrough.html

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</head>
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<body>
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<h1>Pagoda2 Walkthrough</h1>
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<h2>Overview</h2>

‎inst/rookServerDocs/js/aspectsTableViewer.js

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],
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listeners: {
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'selectionchange': genesetSelectionChangeListener
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}
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},
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tbar: Ext.create('Ext.PagingToolbar', {
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displayInfo: true,
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prependButtons: true,
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items: [{
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xtype: 'button',
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glyph: 0xf0c7 , //fa-floppy-o
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tooltip: 'Export Selected',
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handler: function(){
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var grid = Ext.getCmp('genesetsAspectTable');
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var csvContent = "data:text/csv;charset=utf-8\n";
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var columns = grid.columnManager.columns;
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var columnsCount = columns.length;
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for (var i = 0; i < columnsCount; i++) {
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if (!columns[i].hidden) {
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csvContent += columns[i].text + ",";
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}
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}
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csvContent = csvContent.substring(0, csvContent.length-1);
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csvContent += "\r";
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for (var j = 0; j<columnsCount; j++) {
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if(!columns[j].hidden){
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console.log(columns[j]);
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}
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}
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var rows = grid.store.data.items;
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var rowsCount = rows.length;
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for (var i = 0; i < rowsCount; i++) {
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var row = rows[i].data;
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for (var j = 1; j<columnsCount; j++) {
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if (!columns[j].hidden) {
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var value = row[columns[j].dataIndex];
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csvContent += "\"" + value + "\"" + ",";
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}
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}
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csvContent = csvContent.substring(0, csvContent.length-1);
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csvContent += "\r";
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}
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var encodedUri = encodeURI(csvContent);
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var is_safari = navigator.userAgent.toLowerCase().indexOf('safari/') > -1;
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if(!is_safari){
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var link = document.createElement("a");
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link.setAttribute("href", encodedUri);
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link.setAttribute("download", "my_data.csv");
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document.body.appendChild(link); // Required for FF
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link.click(); // This will download the data file named "my_data.csv".
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}else{
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var link = document.createElement("a");
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link.setAttribute("href", encodedUri);
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link.setAttribute("target", "_blank");
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document.body.appendChild(link); // Required for FF
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link.click(); // This will download the data file named "my_data.csv".
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}
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}
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}]
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})
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});
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var selModel = Ext.create('Ext.selection.CheckboxModel', {});
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var genesTableForAspects = Ext.create('Ext.grid.Panel',{
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var geneSelCntr = new geneSelectionController();
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geneSelCntr.setSelection( selectedGeneNames,'geneTableSelection','geneTableSelection');
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var heatmapV = new heatmapViewer();
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heatmapV.setNamedSelectionToDisplayGenes('auto_geneTableSelection');
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heatmapV.drawHeatmap();
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var heatmapV = new heatmapViewer();
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heatmapV.setNamedSelectionToDisplayGenes('auto_geneTableSelection');
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heatmapV.drawHeatmap();
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} // selection change
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}, // listeners
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tbar: Ext.create('Ext.PagingToolbar', {
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displayInfo: true,
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prependButtons: true,
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displayInfo: true,
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prependButtons: true,
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items: [{
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xtype: 'button',
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glyph: 0xf0c7 , //fa-floppy-o
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tooltip: 'Export Selected',
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handler: function(){
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var grid = Ext.getCmp('genesAspectsTable');
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var csvContent = "data:text/csv;charset=utf-8\n";
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var columns = grid.columnManager.columns;
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var columnsCount = columns.length;
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for (var i = 0; i < columnsCount; i++) {
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if (!columns[i].hidden) {
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csvContent += columns[i].text + ",";
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}
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}
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csvContent = csvContent.substring(0, csvContent.length-1);
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csvContent += "\r";
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for (var j = 0; j<columnsCount; j++) {
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if(!columns[j].hidden){
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console.log(columns[j]);
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}
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}
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var rows = grid.store.data.items;
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var rowsCount = rows.length;
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for (var i = 0; i < rowsCount; i++) {
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var row = rows[i].data;
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for (var j = 1; j<columnsCount; j++) {
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if (!columns[j].hidden) {
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var value = row[columns[j].dataIndex];
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csvContent += "\"" + value + "\"" + ",";
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}
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}
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csvContent = csvContent.substring(0, csvContent.length-1);
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csvContent += "\r";
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}
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var encodedUri = encodeURI(csvContent);
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var is_safari = navigator.userAgent.toLowerCase().indexOf('safari/') > -1;
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if(!is_safari){
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var link = document.createElement("a");
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link.setAttribute("href", encodedUri);
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link.setAttribute("download", "my_data.csv");
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document.body.appendChild(link); // Required for FF
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link.click(); // This will download the data file named "my_data.csv".
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}else{
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var link = document.createElement("a");
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link.setAttribute("href", encodedUri);
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link.setAttribute("target", "_blank");
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document.body.appendChild(link); // Required for FF
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link.click(); // This will download the data file named "my_data.csv".
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}
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}
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}] //tbar
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}) //tbar
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});
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areaHolder.add([{
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type: 'panel',
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title: '',

‎inst/rookServerDocs/js/geneSetsTableViewer.js

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displayInfo: true,
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prependButtons: true,
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items: [
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{
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xtype: 'button',
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glyph: 0xf0c7 , //fa-floppy-o
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tooltip: 'Export Selected',
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handler: function(){
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var grid = Ext.getCmp('genesetGenesTable');
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var csvContent = "data:text/csv;charset=utf-8\n";
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var columns = grid.columnManager.columns;
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var columnsCount = columns.length;
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for (var i = 0; i < columnsCount; i++) {
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if (!columns[i].hidden) {
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csvContent += columns[i].text + ",";
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}
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}
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csvContent = csvContent.substring(0, csvContent.length-1);
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csvContent += "\r";
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for (var j = 0; j<columnsCount; j++) {
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if(!columns[j].hidden){
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console.log(columns[j]);
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}
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}
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var rows = grid.store.data.items;
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var rowsCount = rows.length;
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for (var i = 0; i < rowsCount; i++) {
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var row = rows[i].data;
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for (var j = 1; j<columnsCount; j++) {
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if (!columns[j].hidden) {
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var value = row[columns[j].dataIndex];
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csvContent += "\"" + value + "\"" + ",";
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}
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}
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csvContent = csvContent.substring(0, csvContent.length-1);
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csvContent += "\r";
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}
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var encodedUri = encodeURI(csvContent);
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var is_safari = navigator.userAgent.toLowerCase().indexOf('safari/') > -1;
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if(!is_safari){
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var link = document.createElement("a");
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link.setAttribute("href", encodedUri);
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link.setAttribute("download", "my_data.csv");
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document.body.appendChild(link); // Required for FF
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link.click(); // This will download the data file named "my_data.csv".
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}else{
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var link = document.createElement("a");
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link.setAttribute("href", encodedUri);
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link.setAttribute("target", "_blank");
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document.body.appendChild(link); // Required for FF
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link.click(); // This will download the data file named "my_data.csv".
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}
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}
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},
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{
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emptyText: 'Search...',
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xtype: 'textfield',
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} // listeners
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} // search textbox
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}, // search textbox
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] // items
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}) // tbar
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