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Commit b96899a6 authored by NAVRATIL VINCENT's avatar NAVRATIL VINCENT
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LAst update and correction before Bioarxiv

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Showing with 45 additions and 39 deletions
data/dataset_focus/DGINN_dataset_focus.csv
View file @ b96899a6
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shinyapps-virhostevol.io/global.R
View file @ b96899a6
......@@ -12,8 +12,8 @@ library(ggmsa)
library(tidyverse)
library(readr)
print(getwd())
#sudo apt install -y r-cran-shinythemes r-cran-shinycssloaders r-cran-shinycssloaders r-cran-dt r-cran-ggplot2 r-cran-tidyverse r-cran-readr r-cran-biocmanager
##RUN install2.r -e shiny shinythemes shinycssloaders gridextra dt ggplot2 tidyverse readr
colnames <- c("File","Name","Gene","Description","GeneSize","NbSpecies","BUSTED","BUSTED_p-value","MEME_NbSites","MEME_PSS","BppM1M2","BppM1M2_p-value","BppM1M2_NbSites","BppM1M2_PSS","BppM7M8","BppM7M8_p-value","BppM7M8_NbSites","BppM7M8_PSS","codemlM1M2","codemlM1M2_p-value","codemlM1M2_NbSites","codemlM1M2_PSS","codemlM7M8","codemlM7M8_p-value","codemlM7M8_NbSites","codemlM7M8_PSS")
\ No newline at end of file
colnames_focus <- c("File","Name","Gene","Description","GeneSize","NbSpecies","BUSTED","BUSTED_p-value","MEME_NbSites","MEME_PSS","FUBAR","FUBAR_NbSites","FUBAR_PSS","BppM1M2","BppM1M2_p-value","BppM1M2_NbSites","BppM1M2_PSS","BppM7M8","BppM7M8_p-value","BppM7M8_NbSites","BppM7M8_PSS","codemlM1M2","codemlM1M2_p-value","codemlM1M2_NbSites","codemlM1M2_PSS","codemlM7M8","codemlM7M8_p-value","codemlM7M8_NbSites","codemlM7M8_PSS")
colnames_full <- c("File","Name","Gene","Description","GeneSize","NbSpecies","omegaM0Bpp","omegaM0codeml","BUSTED","BUSTED_p-value","MEME_NbSites","MEME_PSS","BppM1M2","BppM1M2_p-value","BppM1M2_NbSites","BppM1M2_PSS","BppM7M8","BppM7M8_p-value","BppM7M8_NbSites","BppM7M8_PSS","codemlM1M2","codemlM1M2_p-value","codemlM1M2_NbSites","codemlM1M2_PSS","codemlM7M8","codemlM7M8_p-value","codemlM7M8_NbSites","codemlM7M8_PSS")
shinyapps-virhostevol.io/server.R
View file @ b96899a6
......@@ -18,14 +18,13 @@ shinyServer(
return(NULL)
}
else{
colnames <- c("File","Name","Gene","Description","GeneSize","NbSpecies","BUSTED","BUSTED_p-value","MEME_NbSites","MEME_PSS","BppM1M2","BppM1M2_p-value","BppM1M2_NbSites","BppM1M2_PSS","BppM7M8","BppM7M8_p-value","BppM7M8_NbSites","BppM7M8_PSS","codemlM1M2","codemlM1M2_p-value","codemlM1M2_NbSites","codemlM1M2_PSS","codemlM7M8","codemlM7M8_p-value","codemlM7M8_NbSites","codemlM7M8_PSS")
df <- read.csv2(dginn_file,sep=",",strip.white = TRUE)
df <- read.csv2(dginn_file,sep=";",strip.white = TRUE)
df <- df[,c(-1)]
names(df) <- colnames
names(df) <- colnames_focus
df$BppM7M8_NbSites <- as.numeric(df$BppM7M8_NbSites)
sel <- df$BppM1M2_NbSites+df$BppM7M8_NbSites+df$codemlM1M2_NbSites+df$codemlM7M8_NbSites
sel <- df$BppM1M2_NbSites+df$BppM7M8_NbSites+df$codemlM1M2_NbSites+df$codemlM7M8_NbSites+df$FUBAR_NbSites
sel <- sel == 0 | is.na(sel)
return(df[!sel,])
......@@ -41,19 +40,19 @@ shinyServer(
return(NULL)
}
else{
colnames <- c("File","Name","Gene","Description","GeneSize","NbSpecies","omegaM0Bpp","omegaM0codeml","BUSTED","BUSTED_p-value","MEME_NbSites","MEME_PSS","BppM1M2","BppM1M2_p-value","BppM1M2_NbSites","BppM1M2_PSS","BppM7M8","BppM7M8_p-value","BppM7M8_NbSites","BppM7M8_PSS","codemlM1M2","codemlM1M2_p-value","codemlM1M2_NbSites","codemlM1M2_PSS","codemlM7M8","codemlM7M8_p-value","codemlM7M8_NbSites","codemlM7M8_PSS")
df <- read.csv2(dginn_file,sep=",")
#split primates and bat data
df_primates <- df[,c(5,6,2,3,7:30)]
df_primates[,2] <- "primates"
names(df_primates) <- colnames
names(df_primates) <- colnames_full
df_bats <- df[,c(31,32,4,3,33:56)]
df_bats[,2] <- "bats"
names(df_bats) <- names(df_primates)
df <- rbind(df_primates,df_bats)
sel <- df$BppM1M2_NbSites+df$BppM7M8_NbSites+df$codemlM1M2_NbSites+df$codemlM7M8_NbSites
sel <- sel == 0 | is.na(sel)
......@@ -201,7 +200,7 @@ shinyServer(
selection = 'single',
rownames= FALSE,
options = list(pageLength = 5, columnDefs = list( list(targets = (colnames %>% str_detect(c("File","PSS")) %>% which())-1, visible = FALSE)))
options = list(pageLength = 5, columnDefs = list( list(targets = c(0,(colnames_focus %>% str_detect(c("PSS")) %>% which())-1), visible = FALSE)))
)
output$dginn_data_full <- DT::renderDataTable({
......@@ -211,7 +210,7 @@ shinyServer(
selection = 'single',
rownames= FALSE,
options = list(pageLength = 5, columnDefs = list( list(targets = (colnames %>% str_detect(c("File","PSS")) %>% which())-1, visible = FALSE)))
options = list(pageLength = 5, columnDefs = list( list(targets = c(0,(colnames_full %>% str_detect(c("PSS")) %>% which())-1), visible = FALSE)))
)
#renderPlotOutput -- ggTree + msa + summary
......@@ -233,7 +232,7 @@ shinyServer(
#
# get dginn_data_model_summary
#
models <- c("MEME","BppM1M2","BppM7M8","codemlM1M2","codemlM7M8")
models <- c("MEME","BppM1M2","BppM7M8","codemlM1M2","codemlM7M8","FUBAR")
dginn_data_model_summary <- list()
dginn_data_model_summary[1] <- c()
......@@ -279,7 +278,7 @@ shinyServer(
insertUI(
selector = "#ggtree_plot_focus",
where = "afterEnd",
ui = downloadLink("tree_focus",".tree")
ui = downloadLink("tree_focus","[family.tree]")
)
removeUI(
......@@ -288,7 +287,7 @@ shinyServer(
insertUI(
selector = "#ggtree_plot_focus",
where = "afterEnd",
ui = downloadLink("msa_focus",".fasta")
ui = downloadLink("msa_focus","[msa.fasta]")
)
}
......
shinyapps-virhostevol.io/ui.R
View file @ b96899a6
......@@ -15,9 +15,9 @@ shinyUI(
),
fluidRow(
div(
column(width = 2, tags$img(src ="logo-ciri.jpg",height=100, style="text-align: center;")),
column(width = 2, tags$img(src ="CIRI-logo.png",height=100, style="text-align: center;")),
column(width = 2, tags$img(src ="Logo_lbbe.png",height=100, style="text-align: center;")),
column(width = 2, tags$img(src ="amsb-logo.png",height=100, style="text-align: center;")),
column(width = 2, tags$img(src ="amsb-logo.png",height=100, style="text-align: center;"))
)
)
),
......@@ -25,7 +25,7 @@ shinyUI(
fluidRow(
column(12,
tags$div(class="header", checked=NA,
HTML('This is the online material of the manuscript entitled <b>"Distinct evolutionary trajectories of SARS-CoV-2 interacting proteins in bats and primates identify host determinants of COVID-19"</b> by Cariou et al. (doi:// to come). <br><br>The <b>"DGINN full dataset"</b> is the result of the automated screens of positive selection on SARS-CoV-2 interacting proteins. When selecting/clicking on a gene, a visualization of corresponding alignments, phylogenetic trees and results of positive selection analyses (genes and sites), as well as links to download original files, are provided.<br><br>The <b>"Genes of focus "</b> is the result of a curated and enriched analysis of genes of interest. A visualization of corresponding alignments, phylogenetic trees and results of positively selection analyses (genes and sites), as well as links to download original files, are provided.')
HTML('<br><br>This is the online supplmentary material of the manuscript entitled <b>"Distinct evolutionary trajectories of SARS-CoV-2 interacting proteins in bats and primates identify host determinants of COVID-19"</b> by Cariou et al. (doi:// to come).<br><br>The <b>"Genes of focus "</b> is the result of a curated and enriched analysis of genes of interest. A visualization of corresponding alignments, phylogenetic trees and results of positively selection analyses (genes and sites), as well as links to download original files, are provided. <br><br>The <b>"DGINN full dataset"</b> is the result of the automated screens of positive selection on SARS-CoV-2 interacting proteins. When selecting/clicking on a gene, a visualization of corresponding alignments, phylogenetic trees and results of positive selection analyses (genes and sites), as well as links to download original files, are provided. <br><br>Bats and primates species tree used in this study are available for download [<a href="./data/bats_sp.tree">bats_species.tree</a>] and [<a href="./data/primates_sp.tree">primates_species.tree</a>] ')
)
)
),
......@@ -103,6 +103,12 @@ shinyUI(
)
)
),
fluidRow(
column(width = 1, tags$div(class="header", checked=NA,
HTML("<b>Hosted by</b>"))),
column(width = 2, tags$img(src ="virhostnet2-banner.svg",height=100, style="text-align: center;"))
)
)
......
shinyapps-virhostevol.io/www/virhostnet2-banner.svg 0 → 100644
View file @ b96899a6
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