fix indexing, csv header

kharchenkolab · Dec 12, 2021 · 81f6bf5 · 81f6bf5
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: pagoda2
 Title: Single Cell Analysis and Differential Expression
-Version: 1.0.7
+Version: 1.0.8
 Authors@R: c(person("Nikolas","Barkas", email="nikolas_barkas@hms.harvard.edu", role="aut"), person("Viktor", "Petukhov", email="viktor.s.petuhov@ya.ru", role="aut"), person("Peter", "Kharchenko", email = "peter_kharchenko@hms.harvard.edu", role = "aut"), person("Simon", "Steiger", email = "simon.steiger@gmail.com", role = "ctb"), person("Evan", "Biederstedt", email="evan.biederstedt@gmail.com", role=c("cre", "aut")))
 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.
 License: GPL-3 

diff --git a/README.md b/README.md
@@ -101,5 +101,5 @@ If you find `pagoda2` useful for your publication, please cite:
 ```
 Nikolas Barkas, Viktor Petukhov, Peter Kharchenko and Evan
 Biederstedt (2021). pagoda2: Single Cell Analysis and Differential
-Expression. R package version 1.0.7.
+Expression. R package version 1.0.8.
 ```
diff --git a/doc/pagoda2.walkthrough.R b/doc/pagoda2.walkthrough.R
@@ -102,7 +102,7 @@ r$plotEmbedding(type='PCA', show.legend=FALSE, mark.groups=TRUE, min.cluster.siz
 
 
 ## ---- fig.height=6, fig.width=6-----------------------------------------------
-r$getEmbedding(type='PCA', embeddingType='tSNE', perplexity=50,verbose=FALSE)
+r$getEmbedding(type='PCA', embeddingType='tSNE', perplexity=50, verbose=FALSE)
 r$plotEmbedding(type='PCA', embeddingType='tSNE', show.legend=FALSE, mark.groups=TRUE, min.cluster.size=1, shuffle.colors=FALSE, font.size=3, alpha=0.3, title='clusters (tSNE)', plot.theme=theme_bw() + theme(plot.title = element_text(hjust = 0.5)))
 
 

diff --git a/doc/pagoda2.walkthrough.Rmd b/doc/pagoda2.walkthrough.Rmd
@@ -193,7 +193,7 @@ r$plotEmbedding(type='PCA', show.legend=FALSE, mark.groups=TRUE, min.cluster.siz
 
 We next can construct and plot a tSNE embedding. (This can take some time to complete.)
 ```{r, fig.height=6, fig.width=6}
-r$getEmbedding(type='PCA', embeddingType='tSNE', perplexity=50,verbose=FALSE)
+r$getEmbedding(type='PCA', embeddingType='tSNE', perplexity=50, verbose=FALSE)
 r$plotEmbedding(type='PCA', embeddingType='tSNE', show.legend=FALSE, mark.groups=TRUE, min.cluster.size=1, shuffle.colors=FALSE, font.size=3, alpha=0.3, title='clusters (tSNE)', plot.theme=theme_bw() + theme(plot.title = element_text(hjust = 0.5)))
 ```
 

diff --git a/doc/pagoda2.walkthrough.html b/doc/pagoda2.walkthrough.html
@@ -475,7 +475,7 @@ <h3>Part 2: Analysing Data with Pagoda2</h3>
 
 <p>We next can construct and plot a tSNE embedding. (This can take some time to complete.)</p>
 
-<pre><code class="r">r$getEmbedding(type=&#39;PCA&#39;, embeddingType=&#39;tSNE&#39;, perplexity=50,verbose=FALSE)
+<pre><code class="r">r$getEmbedding(type=&#39;PCA&#39;, embeddingType=&#39;tSNE&#39;, perplexity=50, verbose=FALSE)
 r$plotEmbedding(type=&#39;PCA&#39;, embeddingType=&#39;tSNE&#39;, show.legend=FALSE, mark.groups=TRUE, min.cluster.size=1, shuffle.colors=FALSE, font.size=3, alpha=0.3, title=&#39;clusters (tSNE)&#39;, plot.theme=theme_bw() + theme(plot.title = element_text(hjust = 0.5)))
 </code></pre>
 

diff --git a/doc/pagoda2.walkthrough.md b/doc/pagoda2.walkthrough.md
@@ -327,7 +327,7 @@ r$plotEmbedding(type='PCA', show.legend=FALSE, mark.groups=TRUE, min.cluster.siz
 We next can construct and plot a tSNE embedding. (This can take some time to complete.)
 
 ```r
-r$getEmbedding(type='PCA', embeddingType='tSNE', perplexity=50,verbose=FALSE)
+r$getEmbedding(type='PCA', embeddingType='tSNE', perplexity=50, verbose=FALSE)
 r$plotEmbedding(type='PCA', embeddingType='tSNE', show.legend=FALSE, mark.groups=TRUE, min.cluster.size=1, shuffle.colors=FALSE, font.size=3, alpha=0.3, title='clusters (tSNE)', plot.theme=theme_bw() + theme(plot.title = element_text(hjust = 0.5)))
 ```
 

diff --git a/inst/rookServerDocs/js/aspectsTableViewer.js b/inst/rookServerDocs/js/aspectsTableViewer.js
@@ -108,7 +108,7 @@ aspectsTableViewer.prototype.generateTables = function() {
             tooltip: 'Export Selected',
             handler: function(){
               var grid = Ext.getCmp('genesetsAspectTable');
-              var csvContent = "data:text/csv;charset=utf-8\n";
+              var csvContent = "data:text/csv; charset=utf-8,";
 
               var columns = grid.columnManager.columns;
               var columnsCount = columns.length;
@@ -117,15 +117,9 @@ aspectsTableViewer.prototype.generateTables = function() {
                       csvContent += columns[i].text + ",";
                   }
               }
-              csvContent = csvContent.substring(0, csvContent.length-1);
+              csvContent = csvContent.substring(0, csvContent.length - 1);
               csvContent += "\r";
 
-              for (var j = 0; j<columnsCount; j++) {
-                  if(!columns[j].hidden){
-                      console.log(columns[j]);
-                  }
-              }
-
               var rows = grid.store.data.items;
               var rowsCount = rows.length;
 
@@ -134,14 +128,13 @@ aspectsTableViewer.prototype.generateTables = function() {
                   for (var j = 0; j<columnsCount; j++) {
                       if (!columns[j].hidden) {
                           var value = row[columns[j].dataIndex];
-                          csvContent += "\"" + value + "\"" + ",";
+                          csvContent += value + ",";
                       }
                   }
-                  csvContent = csvContent.substring(0, csvContent.length-1);
+                  csvContent = csvContent.substring(0, csvContent.length - 1);
                   csvContent += "\r";
               }
 
-
               var encodedUri = encodeURI(csvContent);
               var is_safari = navigator.userAgent.toLowerCase().indexOf('safari/') > -1;
 
@@ -235,7 +228,7 @@ aspectsTableViewer.prototype.generateTables = function() {
 
           for (var i = 0; i < rowsCount; i++) {
               var row = rows[i].data;
-              for (var j = 0; j<columnsCount; j++) {
+              for (var j = 1; j<columnsCount; j++) {
                   if (!columns[j].hidden) {
                       var value = row[columns[j].dataIndex];
                       csvContent += "\"" + value + "\"" + ",";

diff --git a/inst/rookServerDocs/js/geneSetsTableViewer.js b/inst/rookServerDocs/js/geneSetsTableViewer.js
@@ -175,7 +175,7 @@ if (gstv.autoShow) {
 
           for (var i = 0; i < rowsCount; i++) {
               var row = rows[i].data;
-              for (var j = 0; j<columnsCount; j++) {
+              for (var j = 1; j<columnsCount; j++) {
                   if (!columns[j].hidden) {
                       var value = row[columns[j].dataIndex];
                       csvContent += "\"" + value + "\"" + ",";