Commit 4860ff1c authored by Amine  GHOZLANE's avatar Amine GHOZLANE
Browse files

Add publication and debug space for heatmap

parent 625fcc80
......@@ -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)
}
......
......@@ -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")
)))
),
......
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