Commit 255e6cd2 authored by Amine  GHOZLANE's avatar Amine GHOZLANE
Browse files

Debug import volume and add news

parent 4f277dce
......@@ -155,7 +155,7 @@ if(!require(philentropy)){
}
if(!require(PhyloTreeMetaR)){
devtools::install_github("https://github.com/pierreLec/PhyloTreeMetaR.git")
devtools::install_github("pierreLec/PhyloTreeMetaR")
library(PhyloTreeMetaR)
}
......@@ -165,7 +165,7 @@ if(!require(PhyloTreeMetaR)){
# }
# Allow to upload 50M files only shaman server
if(Sys.info()["nodename"] == "shaman"){
if(Sys.info()["nodename"] == "ShinyPro"){
options(shiny.maxRequestSize=50*1024^2)
}else{
# No limit
......
......@@ -239,6 +239,8 @@ Plot_Visu_Krona <- function(input,resDiff,CT_OTU,taxo_table){
# Remove zero counts
# Required for Krona
res = merge_dat[merge_dat[,1]>0,]
#print(input$TaxoSelect)
#print(res)
}
}
return(res)
......@@ -693,7 +695,6 @@ CreateTableTree <- function(input,resDiff,CT_Norm_OTU,taxo_table,VarInt,ind_taxo
val = c()
list.val = list()
counts = CT_Norm_OTU
target = resDiff$target
counts_tmp_combined = NULL
prop_tmp_combined = NULL
......
......@@ -103,11 +103,11 @@ shinyServer(function(input, output,session) {
inFile <- input$fileTree
if (is.null(inFile)) return(NULL)
try(read.tree(inFile$datapath)->data,silent=T)
try(read.tree(inFile$datapath)->data, silent=T)
CheckTree = CheckTreeFile(data)
data = CheckTree$tree
try(readLines(inFile$datapath)->treeseq,silent=T)
return(list(data=data,Error = CheckTree$Error,Warning = CheckTree$Warning, treeseq=treeseq))
try(readLines(inFile$datapath)->treeseq, silent=T)
return(list(data=data, Error=CheckTree$Error, Warning=CheckTree$Warning, treeseq=treeseq))
})
......@@ -120,9 +120,7 @@ shinyServer(function(input, output,session) {
res = infoBox(h6(strong("Phylogenetic tree")), subtitle = h6(strong("Load the phylogenetic tree (optional)")) ,color = "light-blue",width=NULL,fill=TRUE, icon = icon("upload"))
if(!is.null(tree)){
if(!is.null(isolate(input$fileTree))){
res = infoBox(h6(strong("Phylogenetic tree")), subtitle = h6("The phylogenetic has been loaded") ,color = "green",width=NULL,fill=TRUE, icon = icon("thumbs-o-up"))
if(!is.null(tree_tmp$Warning)){
res = infoBox(h6(strong("Phylogenetic tree")), subtitle = h6(tree_tmp$Warning) ,color = "orange",width=NULL,fill=TRUE, icon = icon("warning"))
}
......@@ -2129,7 +2127,14 @@ shinyServer(function(input, output,session) {
if(input$PlotVisuSelect=="Barplot") res = showOutput("PlotVisuBar")
else if(input$PlotVisuSelect=="Heatmap") res = d3heatmapOutput("heatmap", height = input$heightVisu+10, width=ifelse(input$modifwidthVisu,input$widthVisu,"100%"))
else if(input$PlotVisuSelect=="Boxplot") res = plotOutput("Boxplot", height = input$heightVisu+10, width=if(input$modifwidthVisu){input$widthVisu})
else if(input$PlotVisuSelect=="Krona") res= tags$iframe(src=paste0("http://127.0.0.1:5438/?parameter=",KronaR()), height = input$heightVisu+10, width=ifelse(input$modifwidthVisu,input$widthVisu,"100%"), seamless=NA)
else if(input$PlotVisuSelect=="Krona"){
if(Sys.info()["nodename"] == "ShinyPro"){
res= tags$iframe(src=paste0("http://hub05.hosting.pasteur.fr/plechat/KronaRShy/?parameter=",KronaR()), height = input$heightVisu+10, width=ifelse(input$modifwidthVisu,input$widthVisu,"100%"), seamless=NA)
}
else{
res= tags$iframe(src=paste0("http://127.0.0.1:5438/?parameter=",KronaR()), height = input$heightVisu+10, width=ifelse(input$modifwidthVisu,input$widthVisu,"100%"), seamless=NA)
}
}
else if(input$PlotVisuSelect=="Tree") res = treeWeightD3Output('PlotVisuTree', height = input$heightVisu+10,width=ifelse(input$modifwidthVisu,input$widthVisu,"100%"))
else if(input$PlotVisuSelect=="Scatterplot" && !input$AddRegScatter) res = scatterD3Output("ScatterplotD3", height = input$heightVisu+10, width=ifelse(input$modifwidthVisu,input$widthVisu,"100%"))
else if(input$PlotVisuSelect=="Scatterplot" && input$AddRegScatter) res = plotOutput("Scatterplotgg", height = input$heightVisu+10,width=if(input$modifwidthVisu){input$widthVisu})
......
......@@ -106,6 +106,7 @@ body <- dashboardBody(
box(
title = "What's new in SHAMAN", width = NULL, status = "primary",
div(style = 'overflow-y: scroll; height: 550px',
addNews("March 30th 2017","Krona, Phylogeny and bug fixes","Krona and phylogenetic tree plots are now available in visualisation. Several new distance are available in PCOA. The import float count matrices is now ok. We have finaly debugged the export of the relative abundance/normalized matrices."),
addNews("Dec 9th 2016","Phylogenetic tree and stress plot","You can now upload a phylogenetic tree to calculate the unifrac distance (only available at the OTU level).
The stress plot has been added to evaluate the goodness of fit of the NMDS."),
addNews("Nov 22th 2016","New visualization and bug fix","We have implemented a new visualization called tree abundance. Some bugs have been fixed (thanks Carine Rey from ENS)."),
......
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