Commit 0b6a8e0f authored by Amine  GHOZLANE's avatar Amine GHOZLANE
Browse files

Add last paper and remove useless print

parent 1341b3fc
......@@ -175,18 +175,19 @@ CheckTargetModel <- function(input,target,labeled,CT)
Error = NULL
HowTo = NULL
InterVar = input$InterestVar
print(colnames(CT))
labels = rownames(target)
ind = which(colnames(CT)%in%labels)
print(ind)
# InterVar%in%
# uniq_column = (length(which(sapply(target[InterVar], function(x) length(unique(x))) == 1)) > 0)
# uniq_column_names = names(which(sapply(target[InterVar], function(x) length(unique(x))) == 1))
## At least one variable selected
if(is.null(Error) && length(ind)<=1){
Error = "Less than two samples names fit with the counts table"
HowTo = "Check the samples names in the target file. They must be in the first column and must correspond EXACTLY to the names in the count table."
}
#if(is.null(Error) && length(ind)<=1){
# Error = "Less than two samples names fit with the counts table"
# HowTo = "Check the samples names in the target file. They must be in the first column and must correspond EXACTLY to the names in the count table."
#}
## At least one variable selected
if(is.null(Error) && length(InterVar)==0){
Error = "At least one variable must be selected for the model"
......
......@@ -77,7 +77,7 @@ Project_box_result <- function(masque_key,curdir){
column(width=5,
strong(h3("18S annotation process")),
shinydashboard::valueBox(ap$Count[6],tags$strong(tags$h5("Number of OTU annotated by SILVA", style = "width: 70%;")), color = "light-blue", width = NULL,icon = uiOutput("silva_icon")),
shinydashboard::valueBox(ap$Count[8],tags$strong(tags$h5("Number of OTU annotated by RDP", style = "width: 70%;")), color = "light-blue", width = NULL,icon = uiOutput("rdp_icon"))
shinydashboard::valueBox(ap$Count[7],tags$strong(tags$h5("Number of OTU annotated by RDP", style = "width: 70%;")), color = "light-blue", width = NULL,icon = uiOutput("rdp_icon"))
)
}
else if(json_data$type == "23S_28S"){
......
......@@ -56,7 +56,7 @@ shinyServer(function(input, output,session) {
}
#print(data)
if(!is.null(data)){
colnames(data) = gsub("-",".",colnames(data))
#colnames(data) = gsub("-",".",colnames(data))
## Rownames
if(!TRUE%in%duplicated(data[,1])) rownames(data)=data[,1];data=data[,-1]
try(round(data, 0)->data, silent=T)
......@@ -367,30 +367,25 @@ shinyServer(function(input, output,session) {
target = isolate(values$TargetWorking)
labeled= isolate(values$labeled)
taxo = isolate(input$TaxoSelect)
print("here-1")
withProgress(
if(!is.null(data$counts) && !is.null(data$taxo) && nrow(data$counts)>0 && nrow(data$taxo)>0 && !is.null(taxo) && taxo!="..." && !is.null(target))
{
print("here0")
design = GetDesign(isolate(input),target)
print(design)
ChTM = CheckTargetModel(input,target,labeled,data$counts)$Error
if(!is.null(design) && is.null(ChTM))
{
print("here")
tmp = isolate(GetCountsMerge(input,data,taxo,target,design))
ChMC = tmp$Error
if (!is.null(ChMC))
{
print("here_getcount")
#ChMC = tmp$Error
#if (!is.null(ChMC))
#{
counts = tmp$counts
## Filtering the counts
if(isolate(input$AddFilter) && !is.null(isolate(input$SliderThSamp)) && !is.null(isolate(input$SliderThAb)))
{
print("here1")
ind.filter =Filtered_feature(counts,isolate(input$SliderThSamp),isolate(input$SliderThAb))$ind
counts = counts[-ind.filter,]
}
print("here2")
CheckTarget = tmp$CheckTarget
#target = tmp$target
#labeled = tmp$labeled
......@@ -398,7 +393,7 @@ shinyServer(function(input, output,session) {
## OTU table, norm and no norm
CT_noNorm = tmp$CT_noNorm
CT_Norm = tmp$CT_Norm
}
#}
}
}
,message="Merging the counts ...")
......@@ -718,7 +713,7 @@ shinyServer(function(input, output,session) {
## Read the data
try(read.csv(inFile$datapath,sep=input$septarget,header=TRUE)->data,silent=TRUE)
if(!is.null(data))
{
data = as.data.frame(data)
......@@ -2610,7 +2605,7 @@ shinyServer(function(input, output,session) {
labeled = values$labeled
taxo = input$TaxoSelect
ChTM = NULL
## Return NULL if there is no error
if(!is.null(target)) ChTM = CheckTargetModel(input,target,labeled,CT)
if(!is.null(ChTM$Error)) {
......
......@@ -66,6 +66,7 @@ body <- dashboardBody(
tabPanel("Citing SHAMAN",
p("If you use SHAMAN for your project, please cite our first application of SHAMAN in Quereda et al. 2016.",style = "font-family: 'times'; font-si16pt"),
p("Publication using SHAMAN :",style = "font-family: 'times'; font-si18pt; font-style: strong"),
p(a("Diverse laboratory colonies of Aedes aegypti harbor the same adult midgut bacterial microbiome.", href="https://www.ncbi.nlm.nih.gov/pubmed/29587819"), "Dickson LB, Ghozlane A, Volant S, Bouchier C, Ma L, Vega-Rúa A, Dusfour I, Jiolle D, Paupy C, Mayanja MN, Kohl A, Lutwama JJ, Duong V, Lambrechts L; Parasit Vectors 2018",style = "font-family: 'times'; font-si16pt"),
p(a("Characteristics of Fecal Microbiota in Pediatric Crohn’s Disease and Their Dynamic Changes During Infliximab Therapy.", href="https://www.ncbi.nlm.nih.gov/pubmed/29194468"), "Wang Y, Gao X, Ghozlane A, Hu H, Li X, Xiao Y, Li D, Yu G, Zhang T; Journal of Crohn's & colitis 2017",style = "font-family: 'times'; font-si16pt"),
p(a("Carryover effects of larval exposure to different environmental bacteria drive adult trait variation in a mosquito vector.", href="https://www.ncbi.nlm.nih.gov/pubmed/28835919"), "Dickson LB, Jiolle D, Minard G, Moltini-Conclois I, Volant S, Ghozlane A, Bouchier C, Ayala D, Paupy C, Moro CV, Lambrechts L; Science Advances 2017",style = "font-family: 'times'; font-si16pt"),
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.; PNAS 2016",style = "font-family: 'times'; font-si16pt"),
......@@ -80,6 +81,7 @@ body <- dashboardBody(
box(
title = "What's new in SHAMAN", width = NULL, status = "primary",
div(style = 'overflow-y: scroll; height: 550px',
addNews("April 17th 2018","Bioinformatics","The bioinformatic treatment offers a larger access to parameters. We also worked a lot on the documentation."),
addNews("September 4th 2017","Bioinformatics","The bioinformatic treatment of fastq reads is now available in SHAMAN. For now, SHAMAN allows to compute OTU, build an OTU table and annotate them with the last version of the available database. This application is for 16S/18S/23S/28S/ITS sequencing."),
addNews("July 18th 2017","Normalization and visualisation","A new method for normalization called total counts was added. More options have been added to the abundance tree."),
addNews("May 30th 2017","Bug fixes","Some visualization bug with the abundance tree and phylogenetic tree are now fixed. The export of the relative abundance and normalised abundance are now given in the right level. This update prepares the field for the next major release of shaman for June."),
......
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