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Commit b000f324 authored by Amine GHOZLANE's avatar Amine GHOZLANE
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Add tutorial and modification of the home page

parent 723ccfe3
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ui.R
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......@@ -117,9 +117,9 @@ body <- dashboardBody(
tabItem(tabName = "Home",
tabBox(title="Welcome to SHAMAN", id="tabset1", height = "700", width = 12,
tabBox(title="Welcome to SHAMAN", id="tabset1", width = 12,
tabPanel("About", p("SHAMAN is a web interface for the analysis of metagenomic data including the normalization,
tabPanel("About", p("SHAMAN is a SHiny application for Metagenomic ANalysis including the normalization,
the differential analysis and mutiple visualization.",style = "font-family: 'times'; font-si16pt"),
......@@ -149,7 +149,7 @@ 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(", Anna Zhukova",href="mailto:anna.zhukova@pasteur.fr"))
p(a("Christophe Malabat",href="mailto:christophe.malabat@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"),
......@@ -161,9 +161,56 @@ body <- dashboardBody(
tabItem(tabName = "Tutorial",
h2("How to !")
tabBox(title="How to use SHAMAN", id="tabset1", width = 12,
tabPanel("Introduction",
p(" You can test SHAMAN with the dataset from", a("[Tap et al. 2015]",href="http://www.ncbi.nlm.nih.gov/pubmed/26235304"),
", which is available", a("here",target="_blank",href="Alimintest.zip"),"."),
p("The zip archive contains 4 different files :", br(),
"- the otu count matrix : Alimintest_otu_table.csv,", br(),
"- the otu annotation table : Alimintest_otu_table.csv,", br(),
"- the experimental design : Alimintest_target.csv,", br(),
"- the contrast table : Alimintest_contrasts.csv."),
p("Two groups of person follow two strict diet periods that involve the intake of 40g following 10g of fiber per day, or 10g of fiber after a 40g fiber intake period :"),
img(src = "tutorial/FigS1.png",height = 400, width = 700),
p("The 16S rRNA (V3 - V4 regions) from fece samples was sequenced at time stamp : 2, 3, 4 and 5.", br(),
"The analysis will consider the different impact of the different fiber intake and the comparison to patient metabolic data.")),
tabPanel("1-Load 16S data",
p("The first step consist to load the count matrix and the annotation table as follow :"),
p("- Select 'Upload your data'", br(),
"- Load the counts table :",br(), img(src = "tutorial/tutorial_upload1.png"),br(),
"- Load the annotation table :", br(), img(src = "tutorial/tutorial_upload2.png"),br(),
"- When successfully loaded, the tables are accessible as bellow :",br(),
img(src = "tutorial/tutorial_upload3.png"),img(src = "tutorial/tutorial_upload4.png"))),
tabPanel("2-Differential analysis",
p("The second step consist to load the experimental design and the contrast table as follow :"),
p("- Select 'Run differential analysis'",br(),
"- Load the target file :",br(),img(src = "tutorial/tutorial_target.png"),br(),
"- Identify the taxonomy level where the analysis will be performed :",br(),img(src = "tutorial/tutorial_target1.png"),br(),
"- Identify the interactions :",br(),img(src = "tutorial/tutorial_target2.png"),br(),
"- Run the analysis :",br(),img(src = "tutorial/tutorial_target3.png"),br(),
"- When successfully loaded, the tables are accessible as bellow :",br(),img(src = "tutorial/tutorial_target4.png")),
p("- Finaly, load the contrast file :",br(),img(src = "tutorial/tutorial_contraste.png"),br(),
"- Contrasts can be visualized as follow :",br(),img(src = "tutorial/tutorial_contraste1.png"))),
tabPanel("3-Diagnostic plots",
p("'Diagnostic plots' section provides several visualization to control the analysis",br(),
"- Total mapped read count",br(),img(src="tutorial/tutorial_total_barplot.png"),br(),
"- Nul barplot count",br(),img(src="tutorial/tutorial_nul_barplot.png"),br(),
"- Maj taxonomy count",br(),img(src="tutorial/tutorial_maj_taxonomy.png"),br(),
"- Density of counts",br(),img(src="tutorial/tutorial_density.png"),br(),
"- Size factors vs total number of reads",br(),img(src="tutorial/tutorial_size_factor.png"),br(),
"- PCA",br(),img(src="tutorial/tutorial_pca.png"),br(),
"- PCOA",br(),img(src="tutorial/tutorial_pcoa.png"),br(),
"- Clustering",br(),img(src="tutorial/tutorial_clustering.png"))),
tabPanel("4-Differential analysis results",
img(src = "tutorial/tutorial_table.png")),
tabPanel("5-Visualization",
p("'Diagnostic plots' section provides several visualization to control the analysis",br(),
"- Barplot",br(),img(src="tutorial/tutorial_barplot.png"),br(),
"- Heatmap",br(),img(src="tutorial/tutorial_heatmap.png"),br(),
"- Boxplot",br(),img(src="tutorial/tutorial_boxplot.png"),br(),
"- Diversity",br(),img(src="tutorial/tutorial_diversity.png"),br(),
"- Rarefaction",br(),img(src="tutorial/tutorial_rarefaction.png"))))
),
tabItem(tabName = "Upload",
......
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