Add publication and debug space for heatmap

internal.R

@@ -618,7 +618,7 @@ CheckCountsTable <- function(counts)
 
   
   ### PCoA
-  PCoAPlot_meta <-function (input,dds, group_init,col = c("SpringGreen","dodgerblue","black","firebrick1"), plot = "pcoa") 
+  PCoAPlot_meta <-function (input, dds, group_init, col = c("SpringGreen","dodgerblue","black","firebrick1"), plot = "pcoa") 
   {
     cval=c()
     time_set = 0
@@ -1526,7 +1526,7 @@ CheckCountsTable <- function(counts)
       if(input$SensPlotVisu=="Horizontal") log2FC = t(as.matrix(log2FC))
       
       if(!export) res = d3heatmap(log2FC, dendrogram = "row", Rowv = TRUE, Colv = NA, na.rm = TRUE, width = input$widthVisu, height = input$heightVisu, show_grid = FALSE, colors = col, scale = input$scaleHeatmap,cexRow = input$LabelSizeHeatmap,cexCol =input$LabelSizeHeatmap, offsetCol=input$LabelColOffsetHeatmap,offsetRow=input$LabelRowOffsetHeatmap)
-      if(export) res = heatmap.2(log2FC, dendrogram = "none", Rowv = TRUE, Colv = NA, na.rm = TRUE, width = input$widthVisu, height = input$heightVisu, margins=c(12,8), density.info="none", show_grid = FALSE, trace="none", col = col, scale = input$scaleHeatmap,cexRow = input$LabelSizeHeatmap,cexCol =input$LabelSizeHeatmap, offsetCol=input$LabelColOffsetHeatmap,offsetRow=input$LabelRowOffsetHeatmap)
+      if(export) res = heatmap.2(log2FC, dendrogram = "none", Rowv = TRUE, Colv = NA, na.rm = TRUE, width = input$widthVisu, height = input$heightVisu, margins=c(input$lowerMargin,input$rightMargin), density.info="none", show_grid = FALSE, trace="none", col = col, scale = input$scaleHeatmap,cexRow = input$LabelSizeHeatmap,cexCol =input$LabelSizeHeatmap, offsetCol=input$LabelColOffsetHeatmap,offsetRow=input$LabelRowOffsetHeatmap)
       }
     return(res)
   }

ui.R

@@ -112,8 +112,11 @@ body <- dashboardBody(
                             p("Thanks to the following people for patches and other suggestions for improvements:"),
                             p(a("Christophe Malabat, ",href="mailto:christophe.malabat@pasteur.fr"), a("Pierre Lechat, ",href="mailto:pierre.lechat@pasteur.fr"),a("Julien Tap, ",href="mailto:julien.tap@danone.com"),a("Anna Zhukova, ",href="mailto:anna.zhukova@pasteur.fr"), a("Rachel Torchet",href="mailto:rachel.torchet@pasteur.fr"))
                           ),
-                   tabPanel("Citing SHAMAN",p("No papers about SHAMAN have been published yet, but a manuscript is in preparation.",style = "font-family: 'times'; font-si16pt"),
-                            p("For now, if you have any comments, questions or suggestions, or want to use SHAMAN please contact authors", a("here", href="mailto:shaman@pasteur.fr"),".", style = "font-family: 'times'; font-si16pt; color:red")
+                   tabPanel("Citing SHAMAN",
+                   p("No papers about SHAMAN have been published yet, but a manuscript is in preparation.",style = "font-family: 'times'; font-si16pt"),
+                   p("Publication using SHAMAN :",style = "font-family: 'times'; font-si18pt; font-style: strong"),
+                   p(a("A bacteriocin from epidemic Listeria strains alters the host intestinal microbiota to favor infection.", href="http://www.ncbi.nlm.nih.gov/pubmed/27140611"), "Quereda JJ, Dussurget O, Nahori MA, Ghozlane A, Volant S, Dillies MA, Regnault B, Kennedy S, Mondot S, Villoing B, Cossart P, Pizarro-Cerda J.",style = "font-family: 'times'; font-si16pt"),
+                   p("If you have any comments, questions or suggestions, or need help to use SHAMAN, please contact authors", a("here", href="mailto:shaman@pasteur.fr"),".", style = "font-family: 'times'; font-si16pt; color:red")
             )))
     ),