fix data tablebugs

likelet · Sep 8, 2015 · 9c33f6e · 9c33f6e
1 parent f830a84
commit 9c33f6e
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Showing 9 changed files with 24 additions and 12 deletions.
diff --git a/inst/IDEA/Dataexploration.Rmd b/inst/IDEA/Dataexploration.Rmd
@@ -14,7 +14,7 @@ Citation: This work is in process of publishing, citation method will be post he
 
 
 ```{r setup, include=FALSE, echo=FALSE}
-knitr::opts_chunk$set(dev="CairoPNG", fig.width = 9, fig.height = 9, dpi = 72)
+knitr::opts_chunk$set( fig.width = 9, fig.height = 9, dpi = 72)
 ```
 
 ```{r global_options, include=FALSE, echo=FALSE, warning=FALSE}

diff --git a/inst/IDEA/EdgeRAnalysis.Rmd b/inst/IDEA/EdgeRAnalysis.Rmd
@@ -8,7 +8,7 @@ output:
     mathjax: http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML
 ---
 ```{r setup, echo=FALSE}
-knitr::opts_chunk$set(dev="CairoPNG", fig.width = 9, fig.height = 9, dpi = 72)
+knitr::opts_chunk$set( fig.width = 9, fig.height = 9, dpi = 72)
 ```
 This is an R Markdown document for edgeR analysis of [IDEA: Interactive Differential Expression Analyzer](http://idea.biocuckoo.org). Plots in Analysis module (plotted in R [[1](#ref1)] with ggplot2[[2](#ref2)] (all plots except heat maps) and pheatmap[[3](#ref3)]) are presented in HTML file via rmarkdown [[4](#ref4)]. For figures of higher resolution, please download from website directly.    
 Citation: This work is in process of publishing, citation method will be post here as soon as possible. Check out the IDEA website above.    

diff --git a/inst/IDEA/NOIseqAnalysis.Rmd b/inst/IDEA/NOIseqAnalysis.Rmd
@@ -12,7 +12,7 @@ html_document:
 Citation: This work is in process of publishing, citation method will be post here as soon as possible. Check out the IDEA website above.    
 
 ```{r setup, echo=FALSE}
-knitr::opts_chunk$set(dev="CairoPNG", fig.width = 9, fig.height = 9, dpi = 72)
+knitr::opts_chunk$set(fig.width = 9, fig.height = 9, dpi = 72)
 ```
 
 ```{r global_options, include=FALSE, echo=FALSE, warning=FALSE}

diff --git a/inst/IDEA/PoissonseqAnalysis.Rmd b/inst/IDEA/PoissonseqAnalysis.Rmd
@@ -9,7 +9,7 @@ html_document:
 ---
 
 ```{r setup, echo=FALSE}
-knitr::opts_chunk$set(dev="CairoPNG", fig.width = 9, fig.height = 9, dpi = 72)
+knitr::opts_chunk$set( fig.width = 9, fig.height = 9, dpi = 72)
 ``` 
 
   This is an R Markdown document for PoissonSeq analysis of [IDEA: Interactive Differential Expression Analyzer](http://idea.biocuckoo.org). Plots in PoissonSeq analysis module (plotted in R [[1](#ref1)] with pheatmap[[2](#ref2)] (for heat map), PoissonSeq[[3](#ref3)] (for power transformation curve) and ggplot2[[4](#ref4)] (for FDR distribution plot)) are presented in HTML file via rmarkdown [[5](#ref1)]. For figures of higher resolution, please download from website directly.    

diff --git a/inst/IDEA/SAMseqAnalysis.Rmd b/inst/IDEA/SAMseqAnalysis.Rmd
@@ -8,7 +8,7 @@ html_document:
   mathjax: http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML
 ---
 ```{r setup, echo=FALSE}
-knitr::opts_chunk$set(dev="CairoPNG", fig.width = 9, fig.height = 9, dpi = 72)
+knitr::opts_chunk$set( fig.width = 9, fig.height = 9, dpi = 72)
 ```  
   This is an R Markdown document for SAMseq analysis of [IDEA: Interactive Differential Expression Analyzer](http://idea.biocuckoo.org). Plots in SAMseq analysis module (plotted in R [[1](#ref1)] with pheatmap[[2](#ref2)] (for heat map), `samr.plot` in SAMSeq (samr) [[3](#ref3)] (for Q-Q plot) and ggplot2[[4](#ref4)] (for FDR distribution plot)) are presented in HTML file via rmarkdown [[5](#ref5)]. For figures of higher resolution, please download from website directly.   
 

diff --git a/inst/IDEA/combinationAnalysis.Rmd b/inst/IDEA/combinationAnalysis.Rmd
@@ -8,7 +8,7 @@ html_document:
   mathjax: http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML
 ---
 ```{r setup, echo=FALSE}
-knitr::opts_chunk$set(dev="CairoPNG", fig.width = 9, fig.height = 9, dpi = 72)
+knitr::opts_chunk$set( fig.width = 9, fig.height = 9, dpi = 72)
 ```
 This is an R Markdown document for Combination Analysis of [IDEA: Interactive Differential Expression Analyzer](http://idea.biocuckoo.org). The following plots are plotted in R [[1](#ref1)] with ggplot2[[2](#ref2)] (for histogram) and VennDiagram[[3](#ref3)] (for Venn diagram)). This analysis report is presented in HTML via rmarkdown [[4](#ref4)].   
 

diff --git a/inst/IDEA/server.R b/inst/IDEA/server.R
@@ -299,6 +299,7 @@ shinyServer(function(input,output,session){
                  h4("Matrix of experimental design (example)",DiaoTips(2,"Comma-separated file with header information is required ")),
                  NiePrettyDownloadButton("downloadExampleDesignFile",addclass="btn-warning","Download design matrix file"),
                  tags$button(class="btn btn-info","View Example data",onmousedown="toStep(2)")
+
              )
            )
     )
@@ -397,6 +398,14 @@ shinyServer(function(input,output,session){
            )
     )
   })
+
+  v <- reactiveValues(data = NULL)
+  observeEvent(input$test, {
+    v$data <- runif(100)
+  })
+  output$testplot <- renderPlot({
+    hist(v$data)
+  })
   #interest variable
   output$interestvariablesUI<-renderUI({ 
     if(values$design =="MF"){
@@ -2232,7 +2241,7 @@ getPowerCurve<-reactive({
     updateProgressBar(session,"intergretiveProgressbar", value=100,visible = FALSE, animate=TRUE)
     table
 
-  })
+  },escape = FALSE)
   ################################
   #Download Plot
   #BarPlot download

diff --git a/inst/IDEA/ui.R b/inst/IDEA/ui.R
@@ -192,6 +192,7 @@ shinyUI(bootstrapPage(theme = "css/bootstrap.min.css",
 
 
                                       ),
+
                                       div(class="none",id="step2",
                                           div(class="hd-option-upload",
                                               tags$button(type="button",class="back-nav-upload glyphicon glyphicon-chevron-left btn btn-lg",id="btn--back2-nav-upload",onmousedown="toStep(1)"),
@@ -217,8 +218,10 @@ shinyUI(bootstrapPage(theme = "css/bootstrap.min.css",
                                               div(class="panel-data panel panel-default",
 
                                                   div(class="panel-body",
-                                                      div(class="alert alert-success","The first 6 rows of count matrix are shown here. "),
+                                                      div(class="alert alert-success","The first 6 rows of count matrix are shown here. ")
+                                                      ,
                                                       dataTableOutput("rowdatashow")
+
                                                   )
                                               )
                                           )

diff --git a/inst/IDEA/www/js/main.js b/inst/IDEA/www/js/main.js
@@ -49,12 +49,12 @@ function toStep(step_id) {
   // else{
     for (i = 0; i < 4; i++) {
       if (i == step_id) {
-        //      document.getElementById("step" + i).className = "block"; //内容的样式
-        $("div[id=step" + i + "]").show();
+             document.getElementById("step" + i).className = "block"; //内容的样式
+        //$("div[id=step" + i + "]").show();
         $("#refreshbutton").click();
       } else {
-        $("div[id=step" + i + "]").hide();
-        //      document.getElementById("step" + i).className = "none"; //内容不显示
+        //$("div[id=step" + i + "]").hide();
+             document.getElementById("step" + i).className = "none"; //内容不显示
       // }
     }
   }