Commit 6d48df24 authored by Stevenn Volant's avatar Stevenn Volant
Browse files

Merge des branches

Merge branch 'master' of https://projets.pasteur.fr/git/meta16s
parents ad2f3310 311591b3
......@@ -1302,7 +1302,26 @@ output$RunButton <- renderUI({
selectizeInput("VisuVarInt",h6(strong("Select the variables of interest")),int, selected = intSel,multiple = TRUE)
})
#####################################################
##
## KRONA
##
#####################################################
output$krona <- renderTable({
data = dataInput()$data
taxo = input$TaxoSelect
if(!is.null(data$counts) && !is.null(data$taxo) && nrow(data$counts)>0 && nrow(data$taxo)>0 && !is.null(taxo) && taxo!="...")
{
print(data$counts)
krona_table=tempfile(pattern = "krona", tmpdir = tempdir(), fileext = "")
url=paste(krona_table, ".html", sep="")
#system(paste("export PERL5LIB=/home/aghozlan/workspace/META16S_App/KronaTools-2.6/lib:$PERL5LIB; /home/aghozlan/workspace/META10S_App/krona_bin/bin/ktImportText", krona_table))
system(paste("ktImportText", krona_table))
refs <- paste0("<a href='", url, "' target='_blank'>krona</a>")
data.frame(refs)
}
}, sanitize.text.function = function(x) x)
# output$VarIntVisuBP <- renderUI({
#
......
......@@ -61,8 +61,23 @@ sidebar <- dashboardSidebar(
body <- dashboardBody(
tabItems(
tabItem(tabName = "Home",
h2("Bienvenue !")
),
tabBox(title="Welcome to Meta16S", id="tabset1", height = "900px", width = 12,
tabPanel("About", p("Meta16S is a web interface for the analysis of metagenomic data including the normalization,
the differential analysis and mutiple visualization.",style = "font-family: 'times'; font-si16pt"),
p("Meta16S is based on DESeq2 R package", a("[Anders and Huber 2010]", href="http://www.ncbi.nlm.nih.gov/pubmed/20979621"), "for the analysis of metagenomic data, as suggested in", a("[McMurdie and Holmes 2014]",href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3974642/"),
". Meta16S robustly identifies the differential abundant genera with the Generalized Linear Model implemented in DESeq2", a("[Love 2014]", href="http://www.ncbi.nlm.nih.gov/pubmed/25516281"),".
Resulting p-values are adjusted according to the Benjamini and Hochberg procedure [Benjamini and Hochberg 1995].
The PCOA is performed with the", a("ade4 R package",href="http://pbil.univ-lyon1.fr/ade4/"), "and plots are generated with", a("ggplot2",href="http://ggplot2.org/"), "or", a("D3.js packages",href="http://d3js.org/"), ".", style = "font-family: 'times'; font-si16pt")),
tabPanel("Authors", h3("The main contributors to Meta16s:"),
p(a("Stevenn Volant", href="mailto:stevenn.volant"), "(Initiator, coding, testing, documentation, evaluation)"),
p(a("Amine Ghozlane",href="mailto:amine.ghozlane@pasteur.fr"), "(Coding, testing, documentation, feature suggestions)"),
p(a("Pierre Lechat",href="mailto:pierre.lechat@pasteur.fr"), "(Coding, testing, feature suggestions)"),
p(a("Marie-Agnès Dillies",href="mailto:marie-agnes.dillies@pasteur.fr"), "(Evaluation)"),
h3("Acknowledgements"),
p("Thanks to the following people for patches and other suggestions for improvements:"),
p(a("Christophe Malabat",href="mailto:christophe.malabat@pasteur.fr"))),
tabPanel("Citing Meta16S",p("No papers about Meta16s have been published yet, but a manuscript is in preparation."),
p("For now, if you have any comments, questions or suggestions, or want to use meta16s please contact", a("Dr. Marie-Agnès Dillies", href="mailto:marie-agnes.dillies@pasteur.fr"),".", style = "font-family: 'times'; font-si16pt; color:red")))),
tabItem(tabName = "Tutorial",
h2("How to !")
),
......@@ -449,8 +464,10 @@ body <- dashboardBody(
#### Krona plot
tabItem(tabName = "Krona",
fluidRow(
column(width=3,p("Krona plot"))
fluidRow(
column(width=3,tableOutput("krona") )
#includeHTML("file:///home/aghozlan/workspace/META16S_App/www/text.krona.html")
)
)
......
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