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app.R
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app.R
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library(shiny)
library(RCurl)
library(shinyBS)
library(shinyjs)
library(SPARQL)
library(data.table)
library(DT)
library(stringr)
library(plyr)
library(rJava)
library(RGBOLApi)
# Source hyperlink function and directories
sapply(list.files(pattern="[.]R$", path="var/", full.names=TRUE), source)
sapply(list.files(pattern="[.]R$", path="query/", full.names=TRUE), source)
# Point to js file
jsfile <- "www/jsfile.js"
# UI ----------------------------------------------------------------------
ui <- fluidPage(
shinyjs::useShinyjs(),
tags$head(
tags$meta(charset = "UTF-8"),
tags$title("SAPP query"),
tags$script(src = 'jsfile.js'),
tags$link(rel = "stylesheet", type = "text/css", href = "sapp.css"),
tags$link(rel="icon",type="image/png", href ="favicon.ico", sizes="32x32")
),
tags$div(class = "Header",
tags$div(class = "banner", tags$img( src = "CIGENE.png", width = 'auto', height = "50px" ),
tags$img( src = "DS.png", width = 'auto', style = 'position:relative;left:50px;', height = "50px" ) ) ),
navbarPage (
"SAPP Query",
# Reaction NavTab =================================
tabPanel(
"Reaction",
tags$div(class = "content",
tags$div(class = "container setwidth",
fluidRow(
column(4,
tags$form(
class = "form-inline",
tags$div(
class = "form-group",
tagAppendAttributes(
textInput(
"variable",
"EC number query",
width = "125px",
value = "5.4.2.11",
placeholder = NULL
),
`data-proxy-click` = "submit"
),
actionButton("submit", "submit")
)
)),
column(6,
selectInput("select", label = ("Select a species"),
choices = list(
"Salmo salar" = 'http://10.209.0.227:8030/blazegraph/namespace/SalmoDB/sparql',
"Danio rerio" = 'http://10.209.0.227:7955/blazegraph/namespace/ZebraDB/sparql' ),
selected = 'http://10.209.0.227:8030/blazegraph/namespace/SalmoDB/sparql'))
) # Fluid Row ends
) # Div container setwidth
), # Div ends Content
# Reaction DataTables
tags$div(class = "content" ,
tags$div(class = "container tables setwidth",
fluidRow(
column(
12,
mainPanel(
width = 12,
style = "height=100%;width:100%;min-height:600px",
textOutput("exampleOutput"),
bsAlert("alert"),
tabsetPanel(
# Reaction SAPP Tab
tabPanel("SAPP",
tags$div(class = "info",
tags$ul(
tags$li(""),
tags$li("")
)),
dataTableOutput('myTable')
),
# Reaction BLAST TAB
tabPanel("BLAST",
tags$div(class = "info",
tags$ul(
tags$li(textOutput("tool")),
tags$li(textOutput("version"))
)),
dataTableOutput('swissprot_table')
),
# Reaction PRIAM Tab
tabPanel("PRIAM",
tags$div(class = "info",
tags$ul(tags$li(textOutput("tool_priam")),
tags$li(textOutput("version_priam")))),
dataTableOutput('priamdata_table')
),
# Reaction Interpro Tab
tabPanel("Interpro",
tags$div(class = "info",
tags$ul(tags$li(textOutput("tool_interpro")),
tags$li(textOutput("version_interpro")))),
dataTableOutput('interprodata_table')
),
# Reaction EnzDP Tab
tabPanel("EnzDP",
tags$div(class = "info",
tags$ul(
tags$li(textOutput("tool_enzdp")),
tags$li(textOutput("version_enzdp"))
)),
dataTableOutput('enzdp_table')
),
# Reaction Result Summary
tabPanel("Result Summary",
tags$div(class = "info",
tags$ul(
tags$li(""),
tags$li("")
)),
dataTableOutput('resultsummarydata_table')
),
# Reaction Manual Anotation
tabPanel(width ="12", "Manual Annotation",
mainPanel(width = 12,
tabsetPanel(
tabPanel("Input Annotations",
tags$div(class="ma",
tags$div(class = "container",style ="min-height:650px",
fluidRow(
### Input feilds
column(12,
tags$form(class = "form-inline",
tags$div(class="information_top",
h4("Personal information and institute"),
tags$hr(),
tagAppendAttributes(
class ="input_feilds authors",
textInput(
"author",
"Author",
width = "125px",
value = "",
placeholder = NULL
)
)
),
tags$div(class="information_mid",
h4("Annotation information"),
tags$hr(),
tagAppendAttributes(
class ="input_feilds gene",
textInput(
"geneid",
"GeneID",
width = "125px",
value = "0",
placeholder = "Use 0 if geneid is not known"
)
),
tagAppendAttributes(
class ="input_feilds gene_name",
textInput(
"gene_name",
"Gene name",
width = "125px",
value = "",
placeholder = NULL
)),
tagAppendAttributes(
class ="input_feilds protein",
textInput(
"protein",
"Protein",
width = "125px",
value = "",
placeholder = NULL
)
),
tagAppendAttributes(
class ="input_feilds reaction",
textInput(
"reaction",
"Reaction",
width = "125px",
value = "",
placeholder = NULL
)
),
tagAppendAttributes(
class ="input_feilds comment_prot",
textInput(
"comment",
"Comment",
width = "250px",
value = "",
placeholder = NULL
)
)
),
tags$div(class="information_bottom", style ="display:none",
tagAppendAttributes(
class ="input_feilds goterm",
textInput(
"goterm",
"Goterm",
width = "125px",
value = "",
placeholder = NULL
)
),
tagAppendAttributes(
class ="input_feilds doi",
textInput(
"doi",
"Doi",
width = "125px",
value = "",
placeholder = NULL
)
),
tagAppendAttributes(
class ="input_feilds url",
textInput(
"url",
"URL",
width = "125px",
value = "",
placeholder = NULL
)
)
),
tagAppendAttributes(
`data-proxy-click` = "ma_submit",
actionButton("ma_submit", "Submit")
)
)
),#tags from and columns ends
column(6, class="dropdown",
selectInput("select_reaction", label = ("Select a institute"),
choices = list(
"NMBU" = 'NMBU',
"University of Sterling" = 'uos',
"wageningen university" = 'wur' ),
selected = 'NMBU'))
) # Fluid row ends
) # div container ends
) # div ma ends
),
# Viewing the manual annotation output
tabPanel("View", width = 12,
### Gene Database view
column (12,
dataTableOutput('contents')
))
)
)
) # Tabpanel manul annotations ends
) # tabset ends
) # main panel ends
) # column ends
) # Fluid Row
) # Div container tables setwidth ends
) # Div content ends
), # Tab Panel reaction ends
# Protein NavTab =================================
tabPanel(
"Protein",
# Protein Search Feild
tags$div(class = "content",
tags$div(class = "container setwidth",
fluidRow(
column(4,
tags$form(
class = "form-inline",
tags$div(
class = "form-group",
tagAppendAttributes(
textInput(
"variableprot",
"NP number query",
width = "125px",
value = "NP_001130025.1",
placeholder = NULL
),
`data-proxy-click` = "submitprot"
),
actionButton("submitprot", "submit")
)
)),
column(6,
selectInput("select", label = ("Select a species"),
choices = list(
"Salmo salar" = 'http://10.209.0.227:8030/blazegraph/namespace/SalmoDB/sparql',
"Danio rerio" = 'http://10.209.0.227:7955/blazegraph/namespace/ZebraDB/sparql' ),
selected = 'http://10.209.0.227:8030/blazegraph/namespace/SalmoDB/sparql')
)
))),
# Protein DataTables
tags$div(class = "content",
tags$div(class = "container tables setwidth",
fluidRow(
column(
12,
mainPanel(
width = 12,
style = "height=100%;width:100%;;min-height:600px",
textOutput("exampleOutput2"),
bsAlert("alert2"),
tabsetPanel(
# Protein SAPP Tab
tabPanel("SAPP",
tags$div(class = "info",
tags$ul(
tags$li(""),
tags$li("")
)),
dataTableOutput('myTableprot')
),
# Protein BLAST TAB
tabPanel("BLAST",
tags$div(class = "info",
tags$ul(
tags$li(textOutput("tool_blast")),
tags$li(textOutput("version_blast"))
)),
dataTableOutput('blastresult_table')
),
# Protein PRIAM
tabPanel("PRIAM",
tags$div(class = "info",
tags$ul(
tags$li(textOutput("tool_priam_prot")),
tags$li(textOutput("version_priam_prot"))
)),
dataTableOutput('priamprot_table')
),
# Protein SIGNAL IP Tab
tabPanel("SIGNALP",
tags$div(class = "info",
tags$ul(
tags$li(textOutput("tool_signalIP")),
tags$li(textOutput("version_signalIP"))
)),
dataTableOutput('signalIP_table')
),
# Protein Interpro Tab
tabPanel("Interpro",
tags$div(class = "info",
tags$ul(
tags$li(textOutput("tool_interpro_prot")),
tags$li(textOutput("version_interpro_prot"))
)),
dataTableOutput('ipr_table')
),
# Protein Interpro Domains Tab
tabPanel("Interpro Domains ",
tags$div(class = "info",
tags$ul(
tags$li(""),
tags$li("")
)),
dataTableOutput('interpro_table')
),
# Protein Manual Anotation
tabPanel("Manual Annotation",
mainPanel( width = 12,
tabsetPanel(
tabPanel("Input Annotations",
tags$div(class="ma",
tags$div(class = "container",style ="height:650px",
fluidRow(
### Input feilds
column(12,
tags$form(class = "form-inline",
tags$div( #class = "form-group",
tags$div(class="information_top",
h4("Personal information and institute"),
tags$hr(),
tagAppendAttributes(
class ="input_feilds",
textInput(
"author_prot",
"Author",
width = "125px",
value = "",
placeholder = NULL
)
)
),
tags$div(class="information_mid",
h4("Annotation information"),
tags$hr(),
tagAppendAttributes(
class ="input_feilds gene",
textInput(
"geneid_prot",
"GeneID",
width = "125px",
value = "0",
placeholder = "Use 0 if geneid is not known"
)
),
tagAppendAttributes(
class ="input_feilds gene_name",
textInput(
"gene_name_prot",
"Gene name",
width = "125px",
value = "",
placeholder = NULL
)),
tagAppendAttributes(
class ="input_feilds protein",
textInput(
"protein_prot",
"Protein",
width = "125px",
value = "",
placeholder = NULL
)
),
tagAppendAttributes(
class ="input_feilds reaction",
textInput(
"reaction_prot",
"Reaction",
width = "125px",
value = "",
placeholder = NULL
)
),
tagAppendAttributes(
class ="input_feilds comment_prot",
textInput(
"comment_prot",
"Comment",
width = "250px",
value = "",
placeholder = NULL
)
)
),
tags$div(class="information_bottom", style ="display:none",
tagAppendAttributes(
class ="input_feilds goterm",
textInput(
"goterm_prot",
"Goterm",
width = "125px",
value = "",
placeholder = NULL
)
),
tagAppendAttributes(
class ="input_feilds doi",
textInput(
"doi_prot",
"Doi",
width = "125px",
value = "",
placeholder = NULL
)
),
tagAppendAttributes(
class ="input_feilds url",
textInput(
"url_prot",
"URL",
width = "125px",
value = "",
placeholder = NULL
)
)
),
tagAppendAttributes(
`data-proxy-click` = "ma_submit_prot",
actionButton("ma_submit_prot", "Submit")
)
)# tags div end
)
),#tags from and columns ends
column(6, class="dropdown",
selectInput("select_protein", label = ("Select a institute"),
choices = list(
"NMBU" = 'NMBU',
"University of Sterling" = 'uos',
"wageningen university" = 'wur' ),
selected = 'NMBU'))
) # Fluid row ends
) # div container ends
) # div ma ends
),
tabPanel("View", width = 12,
### Reaction Database view
column (12,
dataTableOutput('contents_prot')
)
)
)
)
)
)
)
)
)
)
)
), # Tab ends
# Gene DataTables #############################
tabPanel(
"Gene",
tags$div(class = "content",
tags$div(class = " container setwidth",style ="min-height:650px", # tables ma
mainPanel(width = 12,
tabsetPanel( id ="geneTabset",
tabPanel("Manual Annotation",
fluidRow(
### Input feilds
column(12,
tags$form(class = "form-inline",
tags$div( class = "form-group",
tags$div(class="information_top",
h4("Personal information and institute"),
tags$hr(),
tagAppendAttributes(
class ="input_feilds",
textInput(
"author_gene",
"Author",
width = "125px",
value = "",
placeholder = NULL
)
)
),
tags$div(class="information_mid",
h4("Annotation information"),
tags$hr(),
tagAppendAttributes(
class ="input_feilds gene",
textInput(
"gene_gene",
"GeneID",
width = "125px",
value = "0",
placeholder = "Use 0 if geneid is not known"
)),
tagAppendAttributes(
class ="input_feilds gene_name",
textInput(
"name_gene",
"Gene name",
width = "125px",
value = "",
placeholder = NULL
)),
tagAppendAttributes(
class ="input_feilds protein_name",
textInput(
"name_protein",
"Protein name",
width = "125px",
value = "",
placeholder = NULL
)),
tagAppendAttributes(
class ="input_feilds reaction",
textInput(
"reaction_gene",
"Reaction",
width = "125px",
value = "",
placeholder = NULL
)),
tagAppendAttributes(
class ="input_feilds comment_gene",
textInput(
"comment_gene",
"Comment",
width = "250px",
value = "",
placeholder = NULL
))
),
tags$div(class="information_bottom", style ="display:none",
tagAppendAttributes(
class ="input_feilds goterm",
textInput(
"goterm_gen",
"Goterm",
width = "125px",
value = "",
placeholder = NULL
)
),
tagAppendAttributes(
class ="input_feilds doi",
textInput(
"doi_prot",
"Doi",
width = "125px",
value = "",
placeholder = NULL
)
),
tagAppendAttributes(
class ="input_feilds url",
textInput(
"url_prot",
"URL",
width = "125px",
value = "",
placeholder = NULL
)
)
),
tagAppendAttributes(
`data-proxy-click` = "ma_submit_gene",
actionButton("ma_submit_gene", "Submit")
)
)# tags div end
)
), #tags from and columns ends
column(6, class="dropdown_gene",
selectInput("select_gene", label = ("Select a institute"),
choices = list(
"NMBU" = 'NMBU',
"University of Sterling" = 'uos',
"wageningen university" = 'wur' ),
selected = 'NMBU'))
) # Fluid row ends
),
tabPanel(width = 12, "View annotations", value ="gene_tab",
### Gene Database view
column (12,
dataTableOutput('contents_gene')
))
) # second TabsetPanel ends
) # mainPanel div ends
) # div container ends
) # Gene tabPanel ends
) # TabsetPanel ends
) # Navbar page
) # FluidPAge
# Server ---------------------------------
server <- function(input, output, session){
# Database endpoint
endpoint <- isolate(input$select)
endpoint2 <- "http://10.209.0.133:8080/blazegraph/namespace/ManualAnno/sparql"
# endpoint <- 'http://10.209.0.227:8030/blazegraph/namespace/SalmoDB/sparql'
# ncbiprotein <- 'NP_001130025.1'
# ECnumber <- '5.4.2.11'
output$value <- renderPrint({ input$select })
# Get Date for Manual annotations
# SAPP Reaction ============================
observeEvent(input$submit,{
### Clear all data.frames #############################
results <- NULL;results_interpro <- NULL;results_priam <- NULL;results_uniprot <- NULL;swiss_table <- NULL;enzdp_table <- NULL;results_enzdp<-NULL;
fetch_query <- NULL
ecnumber <- shQuote(ECnumber)
### Open manual annotation blazegraph ###########################
ECnumber <- input$variable
### Querying and rendering Reaction annotations to UI #####################
reaction_query <- paste("
SELECT ?ECnumber ?GeneID ?GeneName ?Protein ?Author ?Date ?Institute ?Comment ?url where {
?gene <http://gbol.life#number> ?GeneID .
?gene <http://gbol.life#gene> ?GeneName .
?gene <http://gbol.life#xref> ?author .
?gene <http://gbol.life#provenance> ?geneProv .
?geneProv <http://gbol.life#origin> ?manR .
?manR <http://www.w3.org/ns/prov#wasGeneratedBy> ?manActive .
?manActive <http://www.w3.org/ns/prov#startedAtTime> ?Date .
?author <http://gbol.life#name> ?Author .
?author <http://www.w3.org/ns/prov#actedOnBehalfOf> ?org .
?org <http://gbol.life#legalName> ?Institute .
?gene <http://gbol.life#note> ?comment .
?comment <http://gbol.life#text> ?Comment .
?gene <http://gbol.life#xref> ?protein .
?protein <http://gbol.life#protein_id> ?Protein .
?gene <http://gbol.life#xref> ?ecnumber .
?ecnumber <http://gbol.life#accession> ",ecnumber," .
?ecnumber <http://gbol.life#accession> ?ECnumber .
}",sep="")
fetch_query <- SPARQL(endpoint2,reaction_query)$results
fetch_query <-as.data.table(fetch_query)
output$contents <- renderDataTable({
fetch_query
})
withProgress(
message = 'Fetching data',
detail = 'This may take a few minutes',
value = 0,
{
Sys.sleep(0.50)
incProgress(0.1, detail = "Starting SAPP query")
# Grab queries from source file
prefixes_all <- source('query/prefixes_reactive.R')
# Extract relevant data from the list.
prefixes <- prefixes_all$value[1]
basequery_interpro <- prefixes_all$value[2]
basequery_priam <- prefixes_all$value[3]
basequery_uniprot <- prefixes_all$value[4]
basequery_enzdp <- prefixes_all$value[5]
### Query functions #############################
queryfun <- function(basequery, ecnumber) { return(sub('4.2.1.11', ecnumber, basequery)) }
rename_head <- function(x){
rename(x, c("?header" = "header", "?colname" = "colname", "?value" = "value", "?feature" = "feature"))
}
# CLean up post requests. New sparql functing has quotes around everything
clean_post <- function(data){
data[, value := sub('"','',value, perl = TRUE)] ; data[, value := sub('".+>','',value, perl = TRUE)]
}
#Test the query and rename columns
results_interpro <- data.table(sparql(endpoint, paste(prefixes, queryfun(basequery_interpro, ECnumber))))
results_interpro <- rename_head(results_interpro)
results_interpro <- clean_post(results_interpro)
results_priam <- data.table(sparql(endpoint, paste(prefixes,queryfun(basequery_priam, ECnumber))))
results_priam <- rename_head(results_priam)
results_priam <- clean_post(results_priam)
results_uniprot <- data.table(sparql(endpoint, paste(prefixes,queryfun(basequery_uniprot, ECnumber))))
results_uniprot <- rename_head(results_uniprot)
results_uniprot <- clean_post(results_uniprot)
results_enzdp <- data.table(sparql(endpoint, paste(prefixes,queryfun(basequery_enzdp, ECnumber))))
results_enzdp <- rename_head(results_enzdp)
results_enzdp <- clean_post(results_enzdp)
incProgress(0.4, detail = "Fetching data")
### Check if dataframes are empty #############################
if (empty(results_interpro) && empty(results_priam) && empty(results_uniprot) == TRUE) {
output$exampleOutput <- renderText({
createAlert(session,"alert","exampleAlert",title = "No Query Found",
content = "The number you enterd is not a valid ECnumber or a EC number wich returned an
empty results", append = FALSE)
})
}
# Build dataframes =================================
else{
### Rename columns #############################
results <- data.table(ldply(.id = "tool",list(Interpro = results_interpro,Priam = results_priam, Blast = results_uniprot,Enzdp = results_enzdp )))
incProgress(0.6, detail = "Building tables")
# in order to get nice tables we replace them.
results <- rename_reaction(results)
### BLAST #############################
if ("Blast" %in% results$tool) {
swiss_table <- dcast(results[tool == 'Blast'], ncbiprotein + feature ~ colname,fun.aggregate = paste,collapse = "__")
# Grab names of tool and version to display in header
swiss_tool <- toupper(swiss_table$tool[1])
swiss_version <- swiss_table$version[1]
# Send swiss_Table to a function that proceses the headers
swiss_table <- blast_reaction_rename(swiss_table)
}else {
swiss_tool <- toupper("N/A"); swiss_version <- "N/A";swiss_table <- noframe()
}
### PRIAM #############################
if ("Priam" %in% results$tool) {
priam_table <- dcast(results[tool == 'Priam'],ncbiprotein + feature ~ colname,fun.aggregate = paste,collapse = "__")
# Save tool and version vales for displaying
priam_tool <- toupper(priam_table$tool[1])
priam_version <- priam_table$version[1]
# Parse priam table
priam_table <- priam_reaction_rename(priam_table)
} else {priam_tool <- "N/A"; priam_version <- "N/A";priam_table <- noframe();}
### InterproScan #############################
if ("Interpro" %in% results$tool) {
interpro_table <-dcast(results[tool == 'Interpro'], ncbiprotein + feature ~ colname)
# Grab tool and version varibles
interpro_tool <- toupper(interpro_table$tool[1])
interpro_version <- interpro_table$version[1]
# Parse interpro_table
interpro_table<-interpro_reaction_rename(interpro_table)
} else {interpro_tool <- "N/A";interpro_version <- "N/A";interpro_table <- noframe();}
### EnzDP #############################
if ("Enzdp" %in% results$tool) {
enzdp_table <-dcast(results[tool == 'Enzdp'], ncbiprotein + feature ~ colname)
enzdp_table[, likelihoodscore := as.numeric(likelihoodscore)]
setorder(enzdp_table, -likelihoodscore)
enzdp_table <- rename(enzdp_table, c("<http://www.biopax.org/release/bp-level3.owl#xref" = "ECurl"))
# Grab the tool and version variables
enzdp_tool <- toupper(enzdp_table$tool[1])
enzdp_version <- enzdp_table$version[1]
# Drop the tool and variable
enzdp_table <- enzdp_table[,.(ncbiprotein,ECurl,likelihoodscore,maxbitscore)]
} else {enzdp_tool <- "N/A"; enzdp_version <- "N/A"; enzdp_table <- noframe();}
### Comparing results across tools #############################
results_summary <-
rbind(results[tool == 'Priam' & colname == 'evalue', list('value' = value), by = c('Ncbiprotein','header', 'tool')],
results[tool == 'Enzdp' & colname == 'likelihoodscore', list('value' = value), by = c('Ncbiprotein','header', 'tool')],
results[tool %in% c('Blast','Interpro') & colname == 'tool', list('value' = .N), by = c('Ncbiprotein','header', 'tool')])
results_summary <-dcast(results_summary,Ncbiprotein + header ~ tool,fill = NA,fun.aggregate = paste,collapse = " ")
# map salmon ncbiproteinid to ncbigeneid
if (file.exists('ncbilink.RData'))
{load('ncbilink.RData')}
else{
# download Salmon gff from NCBI
gff_url <- 'ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF_000233375.1_ICSASG_v2/GCF_000233375.1_ICSASG_v2_genomic.gff.gz'
gff_name <- 'GCF_000233375.1_ICSASG_v2_genomic.gff.gz'
if (!file.exists(gff_name))
#downlod using curl, for some reason the default method is slow in Rstudio but not plain R (both on orion cn5)
download.file(gff_url,gff_name,method='curl')
#process CDS lines from GFF file
gff <- fread(paste('zgrep [[:space:]]CDS[[:space:]]',gff_name))
gff <- gff[V3=='CDS']
ncbigene <- sub('GeneID:','',str_match(gff$V9,'GeneID:[0-9]*'))
ncbiname <- sub('gene=','',str_match(gff$V9,'gene=[a-z,A-Z,0-9]*'))
ncbiprotein <- sub('protein_id=','',str_match(gff$V9,'protein_id=[N,X]P_[0-9]*\\.[0-9]*'))
ncbilink <- data.table(ncbigene,ncbiprotein,ncbiname)
setnames(ncbilink,c('ncbigene','ncbiprotein','ncbiname'))
ncbilink <- unique(ncbilink[!is.na(ncbiprotein)])
save(ncbilink,file='ncbilink.RData')
}
if (file.exists('ncbilink.RData'))
{load('ncbilink.RData')}
else{
#download Salmon gff from NCBI
gff_url <- 'ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF_000233375.1_ICSASG_v2/GCF_000233375.1_ICSASG_v2_genomic.gff.gz'
gff_name <- 'GCF_000233375.1_ICSASG_v2_genomic.gff.gz'
if (!file.exists(gff_name))
#downlod using curl, for some reason the default method is slow in Rstudio but not plain R (both on orion cn5)
download.file(gff_url,gff_name,method='curl')
#process CDS lines from GFF file
gff <- fread(paste('zgrep [[:space:]]CDS[[:space:]]',gff_name))
gff <- gff[V3=='CDS']
ncbigene <- sub('GeneID:','',str_match(gff$V9,'GeneID:[0-9]*'))
ncbiname <- sub('gene=','',str_match(gff$V9,'gene=[a-z,A-Z,0-9]*'))
ncbiprotein <- sub('protein_id=','',str_match(gff$V9,'protein_id=[N,X]P_[0-9]*\\.[0-9]*'))
ncbilink <- data.table(ncbigene,ncbiprotein,ncbiname)
setnames(ncbilink,c('ncbigene','ncbiprotein','ncbiname'))
ncbilink <- unique(ncbilink[!is.na(ncbiprotein)])
save(ncbilink,file='ncbilink.RData')
}
# Adjust types of columns if they are present
try(results_summary[, Interpro := as.numeric(Interpro)])
try(results_summary[, Blast := as.numeric(Blast)])
try(results_summary[is.na(Interpro), Interpro := 0])
try(results_summary[is.na(Blast), Blast := 0])
# results_summary <- merge(ncbilink,results_summary,by.y='Ncbiprotein',by.x='ncbiprotein',all.y=T)
# results_summary[,ncbiprotein:=NULL]
try(setorder(results_summary, -Enzdp))
### Isolate the variables to be renderd #############################
# Send the versions and tools name to header
isolate ({
output$tool <- renderText({ paste("Tool: ",swiss_tool)})
output$version <- renderText({paste("Version: ",swiss_version) })
output$tool_priam <- renderText({ paste("Tool: ",priam_tool)})
output$version_priam <- renderText({paste("Version: ",priam_version) })
output$tool_interpro <- renderText({ paste("Tool: ",interpro_tool)})
output$version_interpro <- renderText({paste("Version: ",interpro_version) })
output$tool_enzdp <- renderText({ paste("Tool: ",enzdp_tool)})
output$version_enzdp <- renderText({paste("Version: ",enzdp_version) })
})
### Start rendering the datatables #############################
incProgress(0.6, detail = "Creating output data")
output$myTable <- renderDataTable(
results,
options = list(
iDisplayLength = 10,
scrollX = TRUE,
fixedColumns = TRUE,
rowCallback = JS(
"function(row, data){",
"var match = anchor(data[6]);",
"$('td:eq(6)', row).html(match)",
"}"
)
)
)
output$swissprot_table <- renderDataTable(
swiss_table,
#extensions = 'Responsive',
options = list(
iDisplayLength = 10,
scrollX = TRUE,
fixedColumns = TRUE,
fnInitComplete = JS(
"function (settings, json){tool_header();}"),
rowCallback = JS(
"function(row, data){",
"if(data[1] =='N/A'){}else{var b_match = anchor(data[1])}",
"$('td:eq(1)', row).html(b_match)",
"if(data[2]=='N/A' ){}else{var match2 = anchor(data[2])}",
"$('td:eq(2)', row).html(match2)",
"}"
)
)
)
output$priamdata_table <- renderDataTable(
priam_table,
# extensions = 'Responsive', # This is for making the table clickable
options = list(
iDisplayLength = 10,
scrollX = TRUE,
fixedColumns = TRUE,
# Add a tooltip to the header after table has finished rendering
fnInitComplete = JS("function (settings, json){
tool_header();
}"),
# Add a anchor tag to the table while rendering
rowCallback = JS(
"function(row, data){",
"if(data[1] =='N/A'){}else{var match = anchor(data[1]);}",
"$('td:eq(1)', row).html(match);",
"if(data[2] =='N/A'){}else{var new_links = urls(data[2])}",
"$('td:eq(2)', row).html(new_links);",
"}"
)
)
)
output$interprodata_table <- renderDataTable(
interpro_table,
options = list(
iDisplayLength = 10,
scrollX = TRUE,
fixedColumns = TRUE,
rowCallback = JS(
"function(row, data){",
"if(data[1] =='N/A'){}else{var match = anchor(data[1]);}",
"$('td:eq(1)', row).html(match)",
"if(data[1] =='N/A'){}else{var match2 = anchor(data[2]);}",
"$('td:eq(2)', row).html(match2)",
"}"
)
)
)
output$enzdp_table <- renderDataTable(
enzdp_table,
options = list(
iDisplayLength = 10,
scrollX = TRUE,
fixedColumns = TRUE,
rowCallback = JS(
"function(row, data){",
"if(data[1] =='N/A'){}else{var match = anchor(data[1]);}",
"$('td:eq(1)', row).html(match)",
"if(data[1] =='N/A'){}else{var new_links = urls(data[2])}",
"$('td:eq(2)', row).html(new_links);",
"}"
)
)