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server.r
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server.r
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########################################################################
# Script written and maintained by:
# Karthick L
# PhD student
# Bioinformatics Division
# National Facility of Marine Cyanobacteria (NFMC)
# Bhanrathidasan University
# Trichy
# email: karthick.lakshman@gmail.com
########################################################################
library(shiny)
options(shiny.maxRequestSize=10*1024^2)
library(graph)
library(Rgraphviz)
library(shinyBS)
library(circlize)
require(Biostrings, quietly = TRUE)
library(shinyIncubator)
library(seqLogo)
source("helper.R")
source('all_sessions.R', local=TRUE)
shinyServer(function(input, output, session) {
observe({
if (input$geneserch==0){ return(NULL)}
input$geneserch
isolate({
gone<-subset(kar,kar$id==input$gene_ser)
updateNumericInput(session=session, inputId="instart", value=as.numeric(gone$start)-4000)
updateNumericInput(session=session, inputId="inend", value=as.numeric(gone$end)+4000)
})
})
observe({
isolate({
updateSelectInput(session=session, "sel_one", choices=paste(syn[,2],syn[,3],syn[,1],sep=" - "))
})
})
output$sliders <- renderUI({
r1<-as.integer(input$instart)
r2<-as.integer(input$inend)
slide<-sliderInput("inslider", "",
min =r1 , max = r2, value = c(r1, r2), step = 50)
})
output$slidersmain <- renderUI({
slide<-sliderInput("inslider2", "",
min =1 , max = 71, value = 2, step = 1,ticks = TRUE)
})
observe({
if (input$pushorfl==0){ return(NULL)}
input$pushorf1
isolate({
updateSliderInput(session=session, inputId="inslider2", value=input$inslider2-1)
})
})
observe({
if (input$pushorfr==0){ return(NULL)}
input$pushorfr
isolate({
updateSliderInput(session=session, inputId="inslider2", value=input$inslider2+1)
})
})
observe({
if (input$regsel==0){ return(NULL)}
if(input$regsel=="twor")
{
updateTextInput(session=session, inputId="instart", value=seg[input$inslider2,2])
updateTextInput(session=session, inputId="inend", value=seg[input$inslider2,3])
} else{
updateTextInput(session=session, inputId="instart", value=1000)
updateTextInput(session=session, inputId="inend", value=10000)
}
})
observe({
if (input$locusserch==0){ return(NULL)}
input$locusserch
isolate({
updateNumericInput(session=session, inputId="instart", value=1000)
updateNumericInput(session=session, inputId="inend", value=10000)
})
})
#-----------------------------------------------------navigator--------------------------------------------------------------
observe({
if (input$twoleft==0){ return(NULL)}
input$twoleft
isolate({
updateNumericInput(session=session, inputId="instart", value=as.numeric(input$instart)-8000)
updateNumericInput(session=session, inputId="inend", value=as.numeric(input$inend)-8000)
})
})
observe({
if (input$oneleft==0){ return(NULL)}
input$oneleft
isolate({
updateNumericInput(session=session, inputId="instart", value=as.numeric(input$instart)-4000)
updateNumericInput(session=session, inputId="inend", value=as.numeric(input$inend)-4000)
})
})
observe({
if (input$tworight==0){ return(NULL)}
input$tworight
isolate({
updateNumericInput(session=session, inputId="instart", value=as.numeric(input$instart)+8000)
updateNumericInput(session=session, inputId="inend", value=as.numeric(input$inend)+8000)
})
})
observe({
if (input$oneright==0){ return(NULL)}
input$oneright
isolate({
updateNumericInput(session=session, inputId="instart", value=as.numeric(input$instart)+4000)
updateNumericInput(session=session, inputId="inend", value=as.numeric(input$inend)+4000)
})
})
observe({
if (input$pushright==0){ return(NULL)}
input$pushright
isolate({
updateNumericInput(session=session, inputId="inend", value=as.numeric(input$inend)+4000)
})
})
observe({
if (input$pushleft==0){ return(NULL)}
input$pushleft
isolate({
updateNumericInput(session=session, inputId="inend", value=as.numeric(input$inend)-4000)
})
})
observe({
if (input$instart<9000 | input$inend<16000){
updateButton(session, "twoleft", disabled = TRUE)}else{updateButton(session, "twoleft", disabled = FALSE)}
})
observe({
if (input$instart<5000 |input$inend<6000){
updateButton(session, "oneleft", disabled = TRUE)}else{updateButton(session, "oneleft", disabled = FALSE)}
})
observe({
if (input$instart<5000){
updateButton(session, "pushleft", disabled = TRUE)}else{updateButton(session, "pushleft", disabled = FALSE)}
})
observe({
if (input$moleft==0){ return(NULL)}
input$moleft
isolate({
updateSliderInput(session=session, inputId="inslider", value=as.numeric(input$inslider)-50)
}) })
observe({
if (input$moright==0){ return(NULL)}
input$moright
isolate({
updateSliderInput(session=session, inputId="inslider", value=as.numeric(input$inslider)+50)
}) })
#-----------------------------------------------------navigator--------------------------------------------------------------
#-----------------------------------------------------plot start--------------------------------------------------------------
plotdata<-reactive({
if(input$inCheckboxGroup=="option1"){
outputclr<-cogc}
else if(input$inCheckboxGroup=="option2"){
outputclr<-kasc} else{
outputclr<-cogc}
})
observe({
segd<-subset(seg,seg$V1==input$circo_input)
res<-paste(segd[,2],"-", segd[,3])
updateTextInput(session=session, inputId="segrang", value=res)
})
observe({
segd<-subset(seg,seg$V1==paste("S",input$inslider2,sep=""))
res<-paste(segd[,2],"-", segd[,3])
updateTextInput(session=session, inputId="segrang2", value=res)
})
output$circo <- renderPlot({
plotd<-plotdata()
if (as.character(input$track)=="TRUE"){data<-get(paste("plotd"))}else{data<-NULL}
if (as.character(input$cog)=="TRUE"){cog<-get(paste("cogc"))}else{cog<-NULL}
if (as.character(input$anno)=="TRUE"){kasc<-get(paste("kasc"))}else{kasc<-NULL}
if (is.null(input$circo1)){ return(NULL)}
input$circo1
isolate({
if (is.null(input$circo_input)){cin<-NULL}else{cin<-paste(input$circo_input)}
mplot<-circo_plot(data,seg,cin,kasc,cog,trunit)
updateProgressBar(session, inputId = "pb2", value = 100, visible = TRUE, color = "standard", striped = TRUE, animate = TRUE)
return(mplot)
})
})
observe({
if (input$circo_input==0){return(NULL)}
input$circo_input
isolate({
createAlert(session, inputId = "alert_anchor",
title = "TITLE GOES HERE",
message = paste(input$circo_input),
type = "warning",
dismiss = TRUE, block = TRUE,
append = TRUE )
})
})
updateTypeAhead(session, inputId = "gene_ser", label = "", choices = kar$id)
sel_gene<-reactive({
gres<-subset(kar,kar$id==input$gene_ser)
return(as.character(gres$name))
})
observe({
if (is.null(sel_gene())){return(NULL)}
isolate({
createAlert(session, inputId = "alert_gene",
title = input$gene_ser,
message = sel_gene(),
type = "success",
dismiss = TRUE,
block = TRUE,
append = FALSE)
})
})
marr<-reactive({
if(input$kgset==TRUE){
kar<-plotdata()
dfg<-data.frame(id=input$inSelectg)
dfg<-data.frame(id=dfg[,1])
kar1<-merge(kar,dfg,by="id")
}else{
kar<-plotdata()
kar1<-subset(kar,kar$start>input$inslider[1] & kar$end < input$inslider[2])}
mdat<-merge(mdata,kar1,by="id",sort=F)
return(mdat)
})
distabb<-reactive({
if (is.null(input$inslider)){ return(NULL)}
if (is.null(input$lend)){ return(NULL)}
kar<-plotdata()
kar1<-subset(kar,kar$start>input$instart & kar$end < input$inend)
kar1<-kar1[order(kar1[,3]), ]
if(input$inend - input$instart>10000){
genecluster(kar1,input$lend)}
})
output$disttab<-renderTable({
if (is.null(input$inslider)){ return(NULL)}
if (is.null(input$lend)){ return(NULL)}
distabb()
})
observe({
updateSelectInput(session=session, inputId="distt", choices=rownames(distabb()))
})
output$stress_hmap<-renderPlot({
if (is.null(input$inslider)){ return(NULL)}
if (is.null(marr())){ return(NULL)}
mdat<-marr()
mdat1<- mdat[,2:9]
mdat1<-as.matrix(mdat1,stringsAsFactors = TRUE)
dimnames(mdat1)<-list(mdat[,1],colnames(mdat1[,1:8]))
rc <- rainbow(nrow(mdat1), start = 0, end = .3)
cc <- rainbow(ncol(mdat1), start = 0, end = .3)
heatmap(mdat1, col = c("red","yellow","green"), scale = "column",
RowSideColors = mdat[,16],
xlab ="", ylab = "",
main = "")
})
output$stress_hmap2<-renderPlot({
if (is.null(input$inslider)){ return(NULL)}
if (is.null(marr())){ return(NULL)}
mdat<-marr()
mdat1<- mdat[,c(15,16)]
mdat2<- table(mdat1[,1])
df<-data.frame(cat=names(mdat2))
colnames(df)<-"cat"
col<-merge(df,mdat1,by="cat")
pie(mdat2,labels=names(mdat2),col=unique(col[,2]), radius = 0.5,cex = 0.8)
})
output$marrtab1<- renderTable({
mdat<-marr()
mdat1<- unique(mdat[,c(15,16)])
#colnames(mdat1)<-c("Genes","High Light","BvsG Light","Osmotic","UV","Temperature","H202","Cold","Salt","strand","Gene Description")
})
output$marrtab<- renderTable({
mdat<-marr()
mdat1<- mdat[,c(1:9,13,14)]
#colnames(mdat1)<-c("Genes","High Light","BvsG Light","Osmotic","UV","Temperature","H202","Cold","Salt","strand","Gene Description")
})
keggs<-reactive({
if(input$kgset==TRUE){
kar<-plotdata()
dfg<-data.frame(id=input$inSelectg)
dfg<-data.frame(id=dfg[,1])
kar1<-merge(kar,dfg,by="id")
}else{
kar<-plotdata()
kar1<-subset(kar,kar$start>input$inslider[1] & kar$end < input$inslider[2])}
mdat<-merge(path,kar1,by="id",sort=F)
return(mdat)
})
output$kegg_map<-renderPlot({
if (is.null(input$inslider)){ return(NULL)}
if (is.null(marr())){ return(NULL)}
gdat<-keggs()
gdat1<- gdat[,c(1,2)]
d<-dist(table(gdat1))
fit <- hclust(d)
plot(fit, main="Go Cluster", xlab=NULL)
})
output$kegg_maptab<-renderTable({
if (is.null(input$inslider)){ return(NULL)}
if (is.null(marr())){ return(NULL)}
gdat<-keggs()
gdat1<- gdat[,c(1,3)]
t(table(gdat1))
})
output$kegg_mappie<-renderPlot({
if (is.null(input$inslider)){ return(NULL)}
if (is.null(marr())){ return(NULL)}
mdat<-keggs()
mdat1<- mdat[,c(1,4)]
mdat2<- table(mdat1[,2])
pie(mdat2,labels=names(mdat2), radius = 0.5,cex = 0.8)
})
gos<-reactive({
if(input$kgset==TRUE){
kar<-plotdata()
dfg<-data.frame(id=input$inSelectg)
dfg<-data.frame(id=dfg[,1])
kar1<-merge(kar,dfg,by="id")
}else{
kar<-plotdata()
kar1<-subset(kar,kar$start>input$inslider[1] & kar$end < input$inslider[2])}
mdat<-merge(sgo,kar1,by="id",sort=F)
return(mdat)
})
output$go_mapfirst<-renderPlot({
if (is.null(input$inslider)){ return(NULL)}
if (is.null(marr())){ return(NULL)}
gdat<-gos()
gdat1<- gdat[,c(1,4)]
d<-dist(table(gdat1))
fit <- hclust(d)
plot(fit, main="Go Cluster", xlab=NULL)
if(input$fitchk==TRUE){
rect.hclust(fit, k=input$fitnumb, border="red")}else{return()}
})
output$go_maptab<-renderTable({
if (is.null(input$inslider)){ return(NULL)}
if (is.null(marr())){ return(NULL)}
gdat<-gos()
gdat1<- gdat[,c(1,4)]
t(table(gdat1))
})
output$go_map<-renderPlot({
if (is.null(input$inslider)){ return(NULL)}
if (is.null(marr())){ return(NULL)}
gdat<-gos()
gdat1<- gdat[,c(1,3)]
gdat2<- princomp(t(table(gdat1)),cor=T)
plot(gdat2,type="lines")
})
output$go_map1<-renderPlot({
if (is.null(input$inslider)){ return(NULL)}
if (is.null(marr())){ return(NULL)}
mdat<-gos()
gdat<-subset(mdat,mdat[,2]==input$gotypep)
gdat1<- gdat[,c(1,3)]
gdat2<- princomp(t(table(gdat1)),cor=T)
biplot(gdat2,cex =0.8,expand=1)
})
output$go_sum<-renderPrint({
if (is.null(input$inslider)){ return(NULL)}
if (is.null(marr())){ return(NULL)}
mdat<-gos()
gdat<-subset(mdat,mdat[,2]==input$gotypep)
gdat1<- gdat[,c(1,3)]
summary(princomp(t(table(gdat1)), cor = TRUE,scores = TRUE))
})
output$go_fit<-renderPrint({
if (is.null(input$inslider)){ return(NULL)}
if (is.null(marr())){ return(NULL)}
mdat<-gos()
gdat<-subset(mdat,mdat[,2]==input$gotypep)
gdat1<- gdat[,c(1,3)]
fit<-(princomp(t(table(gdat1)), cor = TRUE,scores = TRUE))
fit$scores
})
output$go_load<-renderPrint({
if (is.null(input$inslider)){ return(NULL)}
if (is.null(marr())){ return(NULL)}
mdat<-gos()
gdat<-subset(mdat,mdat[,2]==input$gotypep)
gdat1<- gdat[,c(1,3)]
loadings(princomp(t(table(gdat1)), cor = TRUE,scores = TRUE))
})
output$go_pie<-renderPlot({
if (is.null(input$inslider)){ return(NULL)}
if (is.null(marr())){ return(NULL)}
mdat<-gos()
mdat<-subset(mdat,mdat[,2]==input$gotypep)
mdat1<- mdat[,c(1,3)]
mdat2<- table(mdat1[,2])
pie(mdat2,labels=names(mdat2), radius = 0.5,cex = 0.8)
})
updateButtonGroup(session, "btngrp1", toggle = "checkbox", style = "info", size = "small")
createAlert(session, inputId = "alert_anchor", message = "MESSAGE GOES HERE", type = "info", dismiss = TRUE, block = FALSE, append = FALSE )
output$myImage <- renderPlot({
data1<-plotdata()
if (is.null(input$inslider)){ return(NULL)}
else if(input$inslider[2]-input$inslider[1]>80000){
createAlert(session, inputId = "alert_gene", message = "Try to select region with in 80000 range!", type = "warning", dismiss = TRUE, block = FALSE, append = FALSE )}else{
input1 <-input$inslider[1]
input2 <-input$inslider[2]
if (is.null(input$inCheckboxGroup)){cogclr<-NULL}else{cogclr<-input$inCheckboxGroup}
if (as.character(input$gridr)=="TRUE"){grir<-"TRUE"}else{grir<-"FALSE"}
mplot<-plotter(data1,trunit,input1,input2,0.2,1.9,"grey","grey",5,cogclr,grir)
observe({
data1<-subset(data1,data1$start>input1 & data1$start<input2)
updateSelectInput(session=session, inputId="gselect", choices=paste(data1$id,'----',data1$name, sep=""),selected=data1[1,])})
updateProgressBar(session, inputId = "pb3", value = 100, visible = TRUE, color = "standard", striped = TRUE, animate = TRUE)
return(mplot)
}})
output$tabval<- renderTable({
})
output$myImage2 <- renderPlot({
data1<-plotdata()
if (is.null(input$inslider)){ return(NULL)}
input1 <-input$inslider[1]
input2 <-input$inslider[2]
if (is.null(input$tracklist)){trk<-NULL}else{trk<-get(paste(input$tracklist))}
if (as.character(input$gridr)=="TRUE"){grir<-"TRUE"}else{grir<-"FALSE"}
mplot<-track(trk,input1,input2,5,grir)
return(mplot)
})
addPopover(session, id = "searchhelp", title = "Gene Search Box", content = "Use Synechocystic gene symbol. example: sll0528", placement = "right", trigger = "hover")
gene1<-reactive({
data1<-plotdata()
if(is.null(input$kar)){return()}
rownames(data1)<-1:nrow(data1)
if(input$kar[2]<1.1 &input$kar[2]>-1.1){
gene1<-subset(data1,data1$start<input$kar[1] & data1$end >input$kar[1])
}else{return()}
return(gene1)
})
output$tabval<-renderText({
if(is.null(input$instart)){return()}
kar1<-subset(kar,kar$start>input$inslider[1] & kar$end < input$inslider[2])
unique(kar1[,1]) })
output$message <- renderText({
gene1<-gene1()
ou1<-paste("<div id='genebox' style='left:550px; top:180px; border:#c1c1c1; padding:10px; border:1px;'><b>",gene1[,c(1)],"</b>:",gene1[,c(6)],"</div>")
updateTextInput(session=session, inputId="geneid", value=gene1[,c(1)])
return(ou1)
})
output$myImage3 <- renderPlot({
data1<-plotdata()
if (is.null(input$inslider)){ return(NULL)}
input1 <-input$inslider[1]
input2 <-input$inslider[2]
if (as.character(input$gridr)=="TRUE"){grir<-"TRUE"}else{grir<-"FALSE"}
mplot<-gc_content(data1,input1,input2,grir,as.numeric(input$gcnum))
return(mplot)
})
datac <- reactive({
dist <- switch(input$variable,
"Acaryochloris marina MBIC11017_chr" =158333233,
"Acaryochloris marina MBIC11017_pREB1" =158339488,
"Acaryochloris marina MBIC11017_pREB2" =158339871,
"Acaryochloris marina MBIC11017_pREB3" =158340280,
"Acaryochloris marina MBIC11017_pREB4" =158340643,
"Acaryochloris marina MBIC11017_pREB5" =158340917,
"Acaryochloris marina MBIC11017_pREB6" =158341140,
"Acaryochloris marina MBIC11017_pREB7" =158341329,
"Acaryochloris marina MBIC11017_pREB8" =158341503,
"Acaryochloris marina MBIC11017_pREB9" =158341621,
"Anabaena cylindrica PCC 7122_chr" =440679730,
"Anabaena cylindrica PCC 7122_pANACY.01" =440685051,
"Anabaena cylindrica PCC 7122_pANACY.03" =440685202,
"Anabaena cylindrica PCC 7122_pANACY.04" =440685330,
"Anabaena cylindrica PCC 7122_pANACY.06" =440685390,
"Anabaena cylindrica PCC 7122_pANACY.05" =436843263,
"Anabaena cylindrica PCC 7122_pANACY.02" =443329695,
"Anabaena sp. 90_cir" =414075311,
"Anabaena sp. 90_pANA01" =414078960,
"Anabaena sp. 90_pANA02" =414079049,
"Anabaena sp. 90_chr" =414079097,
"Anabaena sp. 90_pANA03" =414079804,
"Anabaena variabilis ATCC 29413_plasmid A" =75812284,
"Anabaena variabilis ATCC 29413_plasmid B" =75812629,
"Anabaena variabilis ATCC 29413_plasmid C" =75812661,
"Anabaena variabilis ATCC 29413_chr" =75906225,
"Anabaena variabilis ATCC 29413_ins element" =292905252,
"Arthrospira platensis NIES-39_chr" =479126419,
"Calothrix sp. PCC 6303_pCAL6303.01" =428303471,
"Calothrix sp. PCC 6303_pCAL6303.02" =428303567,
"Calothrix sp. PCC 6303_chr" =428296779,
"Calothrix sp. PCC 6303_pCAL6303.03" =428303526,
"Calothrix sp. PCC 7507_chr" =427715354,
"Chamaesiphon minutus PCC 6605_chr" =434384225,
"Chamaesiphon minutus PCC 6605_pCHA6605.02" =434389900,
"Chamaesiphon minutus PCC 6605_pCHA6605.01" =436736818,
"Chroococcidiopsis thermalis PCC 7203_chr" =428205073,
"Chroococcidiopsis thermalis PCC 7203_pCHRO.02" =428210482,
"Chroococcidiopsis thermalis PCC 7203_pCHRO.01" =428204730,
"Crinalium epipsammum PCC 9333_pCRI9333.01" =428308248,
"Crinalium epipsammum PCC 9333_pCRI9333.02" =428308292,
"Crinalium epipsammum PCC 9333_pCRI9333.04" =428303616,
"Crinalium epipsammum PCC 9333_pCRI9333.05" =428308343,
"Crinalium epipsammum PCC 9333_pCRI9333.07" =428303659,
"Crinalium epipsammum PCC 9333_chr" =428303693,
"Crinalium epipsammum PCC 9333_pCRI9333.03" =428308168,
"Crinalium epipsammum PCC 9333_pCRI9333.06" =428308218,
"Crinalium epipsammum PCC 9333_pCRI9333.08" =428308241,
"Cyanobacterium aponinum PCC 10605_chr" =428768415,
"Cyanobacterium aponinum PCC 10605_pCYAN10605.01" =428771774,
"Cyanobacterium stanieri PCC 7202_chr" =428771848,
"Cyanobium gracile PCC 6307_chr" =427701340,
"Cyanothece sp. ATCC 51142_plasmid A" =172034820,
"Cyanothece sp. ATCC 51142_plasmid B" =172034859,
"Cyanothece sp. ATCC 51142_plasmid C" =172034885,
"Cyanothece sp. ATCC 51142_plasmid D" =172034905,
"Cyanothece sp. ATCC 51142_cir" =172034917,
"Cyanothece sp. ATCC 51142_linear" =172054853,
"Cyanothece sp. PCC 7424_chr" =218437013,
"Cyanothece sp. PCC 7424_pP742403" =218442241,
"Cyanothece sp. PCC 7424_Pp742404" =218442305,
"Cyanothece sp. PCC 7424_pP742405" =218442325,
"Cyanothece sp. PCC 7424_pP742406" =218442342,
"Cyanothece sp. PCC 7424_Pp742402" =218442435,
"Cyanothece sp. PCC 7424_pP742401" =218442611,
"Cyanothece sp. PCC 7425_pP742501" =219883096,
"Cyanothece sp. PCC 7425_pP742503" =219883409,
"Cyanothece sp. PCC 7425_chr" =220905643,
"Cyanothece sp. PCC 7425_pP742502" =220910610,
"Cyanothece sp. PCC 7822_chr" =307149945,
"Cyanothece sp. PCC 7822_Cy782203" =307149708,
"Cyanothece sp. PCC 7822_Cy782204" =307149679,
"Cyanothece sp. PCC 7822_Cy782205" =307149645,
"Cyanothece sp. PCC 7822_Cy782201" =307591951,
"Cyanothece sp. PCC 7822_Cy782202" =307591289,
"Cyanothece sp. PCC 7822_Cy782206" =307591243,
"Cyanothece sp. PCC 8801_pP880101" =218203844,
"Cyanothece sp. PCC 8801_pP880102" =218203933,
"Cyanothece sp. PCC 8801_chr" =218244892,
"Cyanothece sp. PCC 8801_pP880103" =218249153,
"Cyanothece sp. PCC 8802_pP880201" =256818682,
"Cyanothece sp. PCC 8802_chr" =257057919,
"Cyanothece sp. PCC 8802_pP880202" =257062240,
"Cyanothece sp. PCC 8802_pP880203" =256823861,
"Cyanothece sp. PCC 8802_pP880204" =256823891,
"Cylindrospermum stagnale PCC 7417_pCYLST.02" =434389956,
"Cylindrospermum stagnale PCC 7417_chr" =434402184,
"Cylindrospermum stagnale PCC 7417_pCYLST.03" =434408147,
"Cylindrospermum stagnale PCC 7417_pCYLST.01" =436669979,
"Dactylococcopsis salina PCC 8305_chr" =428778395,
"Geitlerinema sp. PCC 7407_chr" =428223461,
"Gloeobacter kilaueensis JS1_chr" =554634310,
"Gloeobacter violaceus PCC 7421_chr" =37519569,
"Gloeocapsa sp. PCC 7428_chr" =434390831,
"Gloeocapsa sp. PCC 7428_pGLO7428.01" =434395721,
"Gloeocapsa sp. PCC 7428_pGLO7428.04" =434395856,
"Gloeocapsa sp. PCC 7428_pGLO7428.03" =434408186,
"Gloeocapsa sp. PCC 7428_pGLO7428.02" =436735872,
"Halothece sp. PCC 7418_chr" =428774686,
"Leptolyngbya sp. PCC 7376_chr" =427722021,
"Microcoleus sp. PCC 7113_chr" =428308377,
"Microcoleus sp. PCC 7113_pMIC7113.01" =428314405,
"Microcoleus sp. PCC 7113_pMIC7113.03" =428314593,
"Microcoleus sp. PCC 7113_pMIC7113.05" =428314670,
"Microcoleus sp. PCC 7113_pMIC7113.06" =428314511,
"Microcoleus sp. PCC 7113_pMIC7113.08" =428314710,
"Microcoleus sp. PCC 7113_pMIC7113.02" =428314740,
"Microcoleus sp. PCC 7113_pMIC7113.04" =428314544,
"Microcoleus sp. PCC 7113_pMIC7113.07" =428314808,
"Microcystis aeruginosa NIES-843_chr" =166362741,
"'Nostoc azollae' 0708_chr" =298489614,
"'Nostoc azollae' 0708_pAzo01" =298501383,
"'Nostoc azollae' 0708_pAzo02" =298501435,
"Nostoc punctiforme PCC 73102_chr" =186680550,
"Nostoc punctiforme PCC 73102_pNPUN05" =186686638,
"Nostoc punctiforme PCC 73102_pNPUN03" =186686664,
"Nostoc punctiforme PCC 73102_pNPUN01" =186686738,
"Nostoc punctiforme PCC 73102_pNPUN02" =186687048,
"Nostoc punctiforme PCC 73102_pNPUN04" =186686999,
"Nostoc sp. PCC 7107_chr" =427705465,
"Nostoc sp. PCC 7120_pCC7120beta" =17158637,
"Nostoc sp. PCC 7120_pCC7120zeta" =17158061,
"Nostoc sp. PCC 7120_pCC7120gamma" =17227374,
"Nostoc sp. PCC 7120_pCC7120epsilon" =17227465,
"Nostoc sp. PCC 7120_chr" =17227497,
"Nostoc sp. PCC 7120_pCC7120delta" =17232874,
"Nostoc sp. PCC 7120_pCC7120alpha" =17233017,
"Nostoc sp. PCC 7524_pNOS7524.01" =427726395,
"Nostoc sp. PCC 7524_chr" =427727289,
"Nostoc sp. PCC 7524_pNOS7524.02" =427726360,
"Oscillatoria acuminata PCC 6304_chr" =428210537,
"Oscillatoria acuminata PCC 6304_pOSCIL6304.02" =428216242,
"Oscillatoria acuminata PCC 6304_pOSCIL6304.01" =428210485,
"Oscillatoria nigro-viridis PCC 7112_chr" =428315182,
"Oscillatoria nigro-viridis PCC 7112_pOSC7112.02" =428314827,
"Oscillatoria nigro-viridis PCC 7112_pOSC7112.03" =428315019,
"Oscillatoria nigro-viridis PCC 7112_pOSC7112.05" =428320964,
"Oscillatoria nigro-viridis PCC 7112_pOSC7112.01" =428320975,
"Oscillatoria nigro-viridis PCC 7112_pOSC7112.04" =428315127,
"Pleurocapsa sp. PCC 7327_chr" =428200461,
"Prochlorococcus marinus str. AS9601_chr" =123967536,
"Prochlorococcus marinus str. MIT 9211_chr" =159902540,
"Prochlorococcus marinus str. MIT 9215_chr" =157412338,
"Prochlorococcus marinus str. MIT 9301_chr" =126695337,
"Prochlorococcus marinus str. MIT 9303_chr" =124021714,
"Prochlorococcus marinus str. MIT 9312_chr" =78778385,
"Prochlorococcus marinus str. MIT 9313_chr" =33862273,
"Prochlorococcus marinus str. MIT 9515_chr" =123965234,
"Prochlorococcus marinus str. NATL1A_chr" =124024712,
"Prochlorococcus marinus subsp. marinus str. CCMP1375_chr" =33239452,
"Prochlorococcus marinus subsp. pastoris str. CCMP1986_chr" =33860560,
"Pseudanabaena sp. PCC 7367_pPSE7367.01" =428219846,
"Pseudanabaena sp. PCC 7367_chr" =428216284,
"Rivularia sp. PCC 7116_chr" =427733619,
"Rivularia sp. PCC 7116_pRIV7116.01" =427740400,
"Rivularia sp. PCC 7116_pRIV7116.02" =427740454,
"Stanieria cyanosphaera PCC 7437_chr" =434396591,
"Stanieria cyanosphaera PCC 7437_pSTA7437.02" =434401063,
"Stanieria cyanosphaera PCC 7437_pSTA7437.03" =434401190,
"Stanieria cyanosphaera PCC 7437_pSTA7437.01" =434408264,
"Stanieria cyanosphaera PCC 7437_pSTA7437.05" =434408556,
"Stanieria cyanosphaera PCC 7437_pSTA7437.04" =436736068,
"Synechococcus elongatus PCC 6301_chr" =56750010,
"Synechococcus elongatus PCC 7942_plasmid 1" =81230333,
"Synechococcus elongatus PCC 7942_chr" =81298811,
"Synechococcus sp. CC9311_chr" =113952711,
"Synechococcus sp. CC9605_chr" =78211558,
"Synechococcus sp. CC9902_chr" =78183584,
"Synechococcus sp. JA-2-3B'a(2-13)_chr" =86607503,
"Synechococcus sp. JA-3-3Ab_chr" =86604733,
"Synechococcus sp. PCC 6312_chr" =427711179,
"Synechococcus sp. PCC 6312_pSYN6312.01" =427714745,
"Synechococcus sp. PCC 7002_pAQ7" =170076470,
"Synechococcus sp. PCC 7002_chr" =170076636,
"Synechococcus sp. PCC 7002_pAQ1" =170079460,
"Synechococcus sp. PCC 7002_pAQ3" =170079464,
"Synechococcus sp. PCC 7002_pAQ4" =170079482,
"Synechococcus sp. PCC 7002_pAQ5" =170079513,
"Synechococcus sp. PCC 7002_pAQ6" =170079553,
"Synechococcus sp. PCC 7502_pSYN7502.01" =428223389,
"Synechococcus sp. PCC 7502_pSYN7502.02" =428223448,
"Synechococcus sp. PCC 7502_chr" =428220140,
"Synechococcus sp. RCC307_chr" =148241099,
"Synechococcus sp. WH 7803_chr" =148238336,
"Synechococcus sp. WH 8109_chr" =33864539,
"Synechocystis sp. PCC 6803_PsysM" =38505535,
"Synechocystis sp. PCC 6803_pSYSA" =38505668,
"Synechocystis sp. PCC 6803_PsysG" =38505775,
"Synechocystis sp. PCC 6803_PsysX" =38505825,
"Synechocystis sp. PCC 6803_chr" =384435229,
"Synechocystis sp. PCC 6803_chr" =451813329,
"Synechocystis sp. PCC 6803_pSYSA_M" =451816673,
"Synechocystis sp. PCC 6803_pSYSG_M" =451816489,
"Synechocystis sp. PCC 6803_pCA2.4_M" =451816539,
"Synechocystis sp. PCC 6803_pCC5.2_M" =451816781,
"Synechocystis sp. PCC 6803_pSYSM_M" =451816542,
"Synechocystis sp. PCC 6803_pSYSX_M" =451816787,
"Synechocystis sp. PCC 6803_pCB2.4_M" =451816777,
"Synechocystis sp. PCC 6803 substr. GT-I_chr" =383489963,
"Synechocystis sp. PCC 6803 substr. PCC-N_chr" =383324079,
"Synechocystis sp. PCC 6803 substr. PCC-P_chr" =383320909,
"Thermosynechococcus elongatus BP-1_chr" =22297544,
"Thermosynechococcus sp. NK55_chr" =571026788,
"Trichodesmium erythraeum IMS101_chr" =113473942)
dat1<-subset(sid,sid$gi==dist)
dat2<- dat1[order(dat1$start2),]
return(dat2)
})
output$comp_plot<-renderPlot({
if (input$comp_but==0){ return(NULL)}
input$comp_but
isolate({
plot(x=1, y=1, type="h", col="white", xlim=c(as.numeric(input$cone),as.numeric(input$ctwo)), ylim=c(-7,8), xlab="", ylab="", yaxt="n",xaxt="n",bty="n",main=paste("Genome level comparison between Synechocystis Genome VS", input$variable), sub=paste("Synechocystis Genome VS", input$variable))
segments(as.numeric(input$cone), 2, as.numeric(input$ctwo), 2, col="#D00000", lwd=1)
segments(as.numeric(input$cone), -2, as.numeric(input$ctwo), -2, col="#3333CC", lwd=1)
datac<-datac()
rect(datac$start2, -1.5, datac$end2, 1.5, xpd=FALSE , border="#ffffff", col="#cccccc20")
rect(datac$start2, 1.8, datac$end2, 2.5, xpd=FALSE , border="#ffffff", col="#D0000070")
rect(datac$start2, -2.5, datac$end2, -1.8, xpd=FALSE , border="#ffffff", col="#3333CC70")
if(as.numeric(input$ctwo)-as.numeric(input$cone)>8000){
text((datac$start2+datac$end2)/2,-5.2,labels=paste(datac$start1, "-", datac$end1,sep=" "),cex = 1, srt = 90,col = "#666666")
text((datac$start2+datac$end2)/2,5.2,labels=paste(datac$start2, "-", datac$end2,sep=" "),cex = 1, srt = 90,col = "#666666")}
else{
text((datac$start2+datac$end2)/2,-5.2,labels=paste(datac$start1, "-", datac$end1,sep=" "),cex = 1, srt = 0,col = "#666666")
text((datac$start2+datac$end2)/2,5.2,labels=paste(datac$start2, "-", datac$end2,sep=" "),cex = 1, srt = 0,col = "#666666")
}
legend("topright",legend=c("Synechocystis 6803_chr", input$variable),lty=1,lwd=2,col=c("#D00000","#3333CC"),ncol=2,bty="n",cex=1.2,text.col=c("black"),inset=0.01)
})
})
output$comp_table<- renderDataTable({
datac<-datac()[,c(2,3,5,6,7,8,10)]
},options = list(aLengthMenu = c(5, 10, 15,20,25,50), iDisplayLength = 10))
observe({
pathdata<-unique(path$specificpath)
updateSelectInput(session=session, inputId="pathselect", choices=pathdata)
})
output$path_table<- renderDataTable({
pathdata1<-subset(path,path$specificpath==input$pathselect)
pathm<-merge(metapath,pathdata1,by="id")
pathm[,c(1,2,4,5)]
},options = list(aLengthMenu = c(5, 10, 15,20,25,50), iDisplayLength = 10))
createAlert(session, inputId = "blastalert",
message = "Note: Blast table data needs to be loaded from remote site and it will take some time to upload", type = "warning",
dismiss = TRUE,
block = FALSE,
append = FALSE )
blastdata<-reactive({
if (input$blast_data==0){ return(NULL)}
input$blast_data
isolate({
bdat<-read.table("bdata.txt", as.is=T, header=T)
})
})
output$blastplot<-renderPlot({
if (input$blast_data==0){ return(NULL)}
bdata<- blastdata()
plot(x=1, y=1, type="h", col="white", xlim=c(as.numeric(bdata$s_start[1]),as.numeric(bdata$s_end[1])), ylim=c(nrow(bdata),0), xlab="", ylab="", yaxt="n",xaxt="n",bty="n")
for (i in 1:nrow(bdata)){
segments(as.numeric(bdata$q_start[1]), i+1, as.numeric(bdata$q_end[1]), i+1, col="#cccccc80", lwd=1)
}
colr<-list()
for (i in 1:nrow(bdata)){
if(bdata$bit_score[i] <40){colr[i]<-"#000000"}
else if(bdata$bit_score[i] >40 & bdata$bit_score[i] <50){colr[i]<-"#3366FF"}
else if(bdata$bit_score[i] > 50 & bdata$bit_score[i] < 80){colr[i]<-"#336633"}
else if(bdata$bit_score[i] > 80 & bdata$bit_score[i] < 200){colr[i]<-"#CC3399"}
else if(bdata$bit_score[i] >200){colr[i]<-"#CC0033"}
}
colr<-do.call(rbind,colr)
for (i in 1:nrow(bdata)){
rect(bdata$q_start[i], i-0.3+1, bdata$q_end[i], i+0.3+1, xpd=FALSE , border="#ffffff", col=colr[i,])
}
})
#-----------------------------------------------------plot end--------------------------------------------------------------
output$blasttable<- renderDataTable({
blastdata()
},options = list(aLengthMenu = c(5, 10, 15,20,25,50), iDisplayLength = 10))
output$seq_bse<- renderText({
kar<-plotdata()
frag <- Views(fs[[1]], as.numeric(input$inslider[1]) ,as.numeric(input$inslider[2]))
if(input$gen_seq==FALSE & input$gen_seqr==FALSE){
seq_data1<-as.character(frag)}
else if(input$gen_seq==TRUE & input$gen_seqr==FALSE){
seq_data1<-as.character(frag)
kar1<-subset(kar,kar$start>input$inslider[1] & kar$end<input$inslider[2])
kar2<-data.frame(id=kar1$id,start=kar1$start-input$inslider[1],end=kar1$end-input$inslider[1],strand=kar1$strand,name=kar1$name)
paste(">",kar2$id,":",kar2$strand,":",kar2$name,"\n",substring(seq_data1, kar2$start, kar2$end),"\n")}
else if(input$gen_seq==TRUE & input$gen_seqr==TRUE){
seq_data1<-as.character(frag)
kar1<-subset(kar,kar$start>input$inslider[1] & kar$end<input$inslider[2])
kar2<-data.frame(id=kar1$id,start=kar1$start-input$inslider[1],end=kar1$end-input$inslider[1],strand=kar1$strand,name=kar1$name)
kar3<-list()
kar4<-list()
for(i in 1:nrow(kar2)){if(kar2[i,4]=="+"){
kar3[i]<-paste(">",kar2[i,1],":",kar2[i,4],":",kar2[i,5],"\n",substring(seq_data1, kar2[i,2], kar2[i,3]),"\n")}
else{kar4[i]<-paste(">",kar2[i,1],":",kar2[i,4],":",kar2[i,5],"\n",Biostrings::reverseComplement(DNAString(substring(seq_data1, kar2[i,2], kar2[i,3]))),"\n")}}
kar3<-do.call(rbind,kar3)
kar4<-do.call(rbind,kar4)
rbind(kar3,kar4)}
})
output$seq_bse1<- renderText({
kar<-plotdata()
if(input$infuse1==0){return()}
input$infuse1
isolate({
frag <- Views(fs[[1]], as.numeric(input$range_start) ,as.numeric(input$range_end))
seq_data1<-as.character(frag)
})
})
promextractdata<-reactive({
if (input$prominfuse1==0){ return(NULL)}
input$prominfuse1
if(input$ckbinprom==FALSE){
data<-kar}else{
gdb<-data.frame(id=input$inSelectg)
data=merge(kar,gdb,by="id")}
isolate({
plus<-subset(data,data$strand=="+")
plus<-subset(plus,plus$id!="slr0611")
minus<-subset(data,data$strand=="-")
pp<-data.frame(id=plus$id,strand=plus$strand,start=plus$start-as.numeric(input$promrange_end),end=plus$start-as.numeric(input$promrange_start))
mp<-data.frame(id=minus$id,strand=minus$strand,start=minus$start+as.numeric(input$promrange_start),end=minus$start+as.numeric(input$promrange_end))
promp<-Views(fs[[1]],pp$start,pp$end)
promn<-Views(fs[[1]],mp$start,mp$end)
pp1<-data.frame(pp,seq=as.character(promp))
mp1<-data.frame(mp,seq=as.character(promn))
prom<-rbind(pp1,mp1)
op<-prom[order(prom[,3]), ]
return(op)
})
})
output$promtable1<- renderDataTable({
promextractdata()
},options = list(aLengthMenu = c(5, 10, 15,20,25,50), iDisplayLength = 10))
output$promextractdown<- downloadHandler(
# This function returns a string which tells the client
# browser what name to use when saving the file.
filename = function() {
paste(input$dataset, input$filetype2, sep = ".")
},
# This function should write data to a file given to it by
# the argument 'file'.
content = function(file) {
sep <- switch(input$filetype2, "csv" = ",", "txt" = "\t")
# Write to a file specified by the 'file' argument
write.table(promextractdata(), file, sep = sep,
row.names = FALSE)
}
)
#--------------------------------------------------------------- sequence extract end------------------------------
#--------------------------------------------------------------- Pattern search start------------------------------
plotCov <- function(cov, start, end, mycol="red") {
plot.new()
plot.window(c(start, end), c(0, 3))
axis(1)
lines(start:end, cov[start:end], type="l", col=mycol)}