Commit 379fa91c authored by NAVRATIL VINCENT's avatar NAVRATIL VINCENT
Browse files

Add Logo and change layout

parent 03581698
renv::restore()
library(shinythemes)
library(shiny)
library(ggtree)
library(ggplot2)
library(shinythemes)
library(shinycssloaders)
library(gridExtra)
library(DT)
library(ggplot2)
library(ggtree)
library(ggmsa)
library(readr)
......@@ -138,7 +138,7 @@ shinyServer(
#
# get dginn_data_model_summary
#
models <- c("BppM1M2","BppM7M8","codemlM1M2","codemlM7M8")
models <- c("MEME","BppM1M2","BppM7M8","codemlM1M2","codemlM7M8")
dginn_data_model_summary <- list()
dginn_data_model_summary[1] <- c()
......@@ -229,9 +229,11 @@ shinyServer(
file_url=paste(path,species,file,sep="/")
tree=read.tree(paste(file_url,".phylip_phyml_tree.txt",sep=""))
site <- dginn_site_df_reactive()[selected_site,"site"]
ggmsa(paste(file_url,".best.fas",sep=""), site-3, site+3, color = "Chemistry_NT", seq_name = T,consensus_views = FALSE, disagreement = FALSE)+ geom_seqlogo()+ geom_msaBar()
site <- dginn_site_df_reactive()[selected_site,"site"]*3
codon_size <- 2
codon_window <- 2
msa_path <- paste(file_url,".best.fas",sep="")
ggmsa(msa_path, site-codon_size-(codon_window*3), site+(codon_window*3), color = "Chemistry_NT", seq_name = T,consensus_views = TRUE, disagreement = FALSE)+ geom_seqlogo()+ geom_msaBar()
#p <- ggtree(tree) + geom_tiplab()
......@@ -250,6 +252,7 @@ shinyServer(
write(tree_data_reactive(), file)
}
)
output$msa <- downloadHandler(
filename = function() {
paste0(input$msa, ".msa")
......
......@@ -2,48 +2,78 @@
# Define UI for application that draws a histogram
shinyUI(
fluidPage(
theme = shinytheme("cerulean"),
lang = "en",
fluidRow(
# Application title
titlePanel("VirHostEvol - Positive selection on genes encoding the SARSCov-2 Viral Interaction Proteins."),
titlePanel(
"VirHostEvol - Browse Positive Selection Sites (PSS) along CDS encoding the SARSCov-2 Viral Interaction Proteins."
),
fluidRow(
div(
column(width = 2, tags$img(src ="https://www.sfr-biosciences.fr/medias/images/seminaires/logo-seminaires/logo-ciri.jpg",height=100, style="text-align: center;")),
column(width = 2, tags$img(src ="https://upload.wikimedia.org/wikipedia/fr/7/7d/Logo_lbbe.png",height=100, style="text-align: center;")),
column(width = 2, tags$img(src ="http://amsb.prabi.fr/amsb-logo.png",height=100, style="text-align: center;")),
) )
),
# Sidebar with a slider input for number of bins
sidebarLayout(
sidebarPanel(
fluidRow(
column(12,
tags$div(class="header", checked=NA,
HTML("Online supplementary materials of the manuscript entitled <b>'Evolutionary history of SARS-CoV-2 interacting proteins in primates and bats reveals major host determinants, including TMPRSS2, FYCO1, RIPK1, and TBK1.'</b> by Cariou M. et <i>al.</i><br><br>Add other informatio stuff ..."),
HTML("This is the online supplementary materials of the manuscript entitled <b>'Evolutionary history of SARS-CoV-2 interacting proteins in primates and bats reveals major host determinants, including TMPRSS2, FYCO1, RIPK1, and TBK1.'</b> by Cariou M. et <i>al.</i><br>doi://<br>Add other informatio stuff ...")
)
)
),
br(),
# Show a plot of the generated distribution
mainPanel(
fluidRow(
column(12,
tabsetPanel(type = "tabs",
tabPanel("DGINN dataset",
tabPanel("DGINN full dataset",
tags$div(class="header", checked=NA,
HTML("<br><br><b>Please select a row</b> to visualise candidates PSS on top of a simplified Multiple Sequence Alignment.<br>At the bottom of the phylogenetic tree and MSA, users can download data by following the <b>.tree</b> and <b>.fas</b> hyperlinks. </br>Add other informatio stuff ...<br><br>")),
DT::dataTableOutput("dginn_data"),
HTML("<br><br><b>Please select/click on a row</b> to visualise candidates PSS infered by DGINN [https://doi.org/10.1093/nar/gkaa680] on top of a simplified Multiple Sequence Alignment (MSA).<br>At the bottom of the phylogenetic tree and MSA, users can download data by following the <b><i>.tree</i></b> and <b><i>.fas</i></b> hyperlinks.
</br>Add other informatio stuff ...<br><br>")),
shinycssloaders::withSpinner(
DT::dataTableOutput("dginn_data")
),
tags$div(class="header", checked=NA,
HTML("<br><br><b>Table: DGINN gene summary table.</b> This table is the output of DGINN software [REF] and highlights the nucleotide sites under positive selection (PSS) infered by the BppM1M2, BppM7M8, codemlM1M2, codemlM7M8 models in either primates and bats taxonomic lineages for a selection of genes encoding SARSCov-2 Viral Interacting Proteins (aka VIP) identified by the Krogan Lab.")),
plotOutput("ggtree_plot",height = "800px"),
HTML("<br><br><b>Table: DGINN gene summary table.</b> This table is the output of DGINN and highlights the nucleotide sites under positive selection (PSS) infered at the codon level by the BppM1M2, BppM7M8, codemlM1M2, codemlM7M8 models in either primates and bats taxonomic lineages for a selection of genes encoding SARSCov-2 Viral Interacting Proteins (aka VIP) identified by the Krogan Laboratory [https://doi.org/10.1038/s41586-020-2286-9].")),
shinycssloaders::withSpinner(
plotOutput("ggtree_plot",height = "800px")
),
tags$div(class="header", checked=NA,
HTML("<br><br><b>Figure: Phylogenetic tree + MSA</b>. This is a back to back representation of the phylogentic tree and a simplified MSA where lightgrey and darkgrey regions of the MSA correspond respectively to substitution and insertion/deletion events.<br><br>")),
tags$div(class="header", checked=NA,
HTML("<br><br><b>Please select a row</b> to visualise candidates sites in the context of the MSA.<br><br>")),
DT::dataTableOutput("dginn_site_data"),
shinycssloaders::withSpinner(
DT::dataTableOutput("dginn_site_data")
),
tags$div(class="header", checked=NA,
HTML("<br><br><b>Table: DGINN output by PSS.</b>This table contains a list of candidate PSS with their p-values.")),
plotOutput("ggtree_ggmsa_site_plot",width="400px",height = "800px"),
shinycssloaders::withSpinner(
plotOutput("ggtree_ggmsa_site_plot",width="400px",height = "800px")
),
tags$div(class="header", checked=NA,
HTML("<br><br><b>Figure PSS MSA.</b> This is a representation of the MSA around the candidate PSS.<br><br>")),
HTML("<br><br><b>Figure PSS MSA.</b> This is a representation of the nucleotide MSA around the candidate PSS codon.<br><br>"))
),
tabPanel("DGINN dataset 2","")
#, radioButtons("model_parameter_rb", label = "Select model:",choices = list("BppM1M2","BppM7M8","BppDFP07_0DFP07","codemlM1M2","codemlM7M8"), selected = "BppM1M2")
)
)
)
)
)
)
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