Merge pull request #76 from gdancik/master

merge with current shinyGEO version

Author: jasdumas

server.R

@@ -1,8 +1,8 @@
 TRACE = FALSE 
-shinycat <-function(...) {
+shinycat <<-function(...) {
 	if (TRACE) cat(...)
 }
-shinyprint <-function(...) print(...)
+shinyprint <<-function(...) print(...)
 
 shinycat("begin source server.R\n")
 source("server/settings.R")

server/server-selection.R

@@ -155,7 +155,10 @@ shinyjs::onclick("btnSelection", {
   }
 
   add.code(code)
-  add.code("data.p = data.p[keep,drop = FALSE]")
+  add.code("data.p = data.p[keep,, drop = FALSE]")
+  add.code("m = match(rownames(data.p), colnames(data.expr))")
+  add.code("data.expr = data.expr[,m,drop = FALSE]\n")
+  
 
  if (!is.null(sel2)) {
 	sel1 = paste0(sel1, "<br>", sel2, "</br>")

server/settings.R

@@ -6,8 +6,8 @@ TEST.DATA = FALSE
 if (TEST.DATA) {
   shinycat("loading test data...\n")
   #load RData/GSE13.RData or RData/GSE19915.RData here
-  load("RData/GSE19915.RData")
+  #load("RData/GSE19915.RData")
   #load("RData/GSE13.RData")
-  #load("RData/GSE13507.RData")
+  load("RData/GSE13507.RData")
 }
 

ui/ui.dashboard.body.R

@@ -109,7 +109,7 @@ body = dashboardBody(
 
 
   shinyjs::useShinyjs(),
-  summaryBSModal("summaryBSModal","Clinical Data","ClinicalDataBtn", size = "large",  
+  summaryBSModal("summaryBSModal","Sample Data","ClinicalDataBtn", size = "large",  
 
     tabsetPanel(id = "tabClinicalData",
 	tabPanel("Summary View", DT::dataTableOutput("summaryModalTable")),

ui/ui.tab.about.R

@@ -8,7 +8,7 @@ tab.about = tabItem("About",
          is a MSc. Graduate Student in the Predictive Analytics program at DePaul University (Chicago, IL/ Online).
          Jasmine has a BSE in Biomedical Engineering from the University of Hartford
          and a Professional Certificate in Medical Product Develpment from UCI Extension.
-         <a href ='https://github.com/jasdumas'>Github Profile</a> <span class= \'label label-primary\'>Package Maintainer</span> </p>
+         <a href ='https://github.com/jasdumas'>Github Profile</a> <span class= \'label label-primary\'>Contributor</span> </p>
     <p><span style = \'font-weight: bold\'> Garrett M. Dancik, PhD </span>
         is an Assistant Professor of Computer Science / Bioinformatics at Eastern
         Connecticut State University (Wilimantic, CT). His research involves applying statistical, mathematical,

ui/ui.tab.reproducible.R

@@ -4,9 +4,9 @@
 
 tab.code =  tabItem("Code",
              h3("R Code"),
- 	     actionButton("reportBtn", "Generate Report"),p(),
-    	     bsModalNoClose("reportModal", "Report Generation", "reportBtn", size = "large",
-		bsAlert("reportAlert")
-    	     ),
+# 	     actionButton("reportBtn", "Generate Report"),p(),
+#    	     bsModalNoClose("reportModal", "Report Generation", "reportBtn", size = "large",
+#		bsAlert("reportAlert")
+#    	     ),
              aceEditor("rmd", mode="markdown", value='',readOnly=T, height="500px")
 )