Nothing
options(shiny.maxRequestSize=100*1024^2)
library(shiny)
library(xcms)
library(enviGCMS)
data("sccp")
shinyServer(function(input, output) {
liststd <- eventReactive(input$go, {
if (!is.null(input$Standards)){
n <- length(input$Standards$datapath)
list <- list()
for(i in 1:n){
file <- xcmsRaw(input$Standards$datapath[i],profstep = 0.1)
list[[i]] <- getareastd(file,ismz = input$ISmz,ppm = input$ppm, con = input$con, rt = input$SCCPrt, rts = input$ISrt)
}}
list
})
output$reg <- renderTable({
li <- liststd()
pCl <- vapply(li,function(x) x$sumpCl,1)
rarea <- vapply(li,function(x) x$sumrarea,1)
t <- summary(lm(rarea~pCl))
t$coefficients
})
output$reg2 <- renderTable({
li <- liststd()
pCl <- vapply(li,function(x) x$sumpCl,1)
rarea <- vapply(li,function(x) x$sumrarea,,1)
t <- summary(lm(rarea~pCl))
t$coefficients
})
output$plotstd <- renderPlot({
li <- liststd()
pCl <- vapply(li,function(x) x$sumpCl,1)
rarea <- vapply(li,function(x) x$sumrarea,1)
plot(rarea~pCl,xlab = 'Chlorine content %', ylab = 'Response Factor', pch = 19)
})
output$plotcomp <- renderPlot({
li <- liststd()
ccomp <- lapply(li,function(x) x$ccomp)
clcomp <- lapply(li,function(x) x$clcomp)
par(mfrow = c(length(ccomp),2),mar=c(1,1,1,1))
for(i in seq_along(ccomp)){
ccompi <- ccomp[[i]]
clcompi <- clcomp[[i]]
barplot(ccompi[,2],names.arg = ccompi[,1],main = paste0('Standard',i,"'s C Composition"))
barplot(clcompi[,2],names.arg = clcompi[,1], main = paste0('Standard',i,"'s Cl Composition"))
}
})
listsample <- eventReactive(input$go2, {
if (!is.null(input$Samples)){
n <- length(input$Samples$datapath)
list <- list()
for(i in 1:n){
file <- xcmsRaw(input$Samples$datapath[i],profstep = 0.1)
list[[i]] <- getarea(file,ismz = input$ISmz,ppm = input$ppm, rt = input$SCCPrt, rts = input$ISrt)
}}
list
})
output$plotcomps <- renderPlot({
li <- listsample()
ccomp <- lapply(li,function(x) x$ccomp)
clcomp <- lapply(li,function(x) x$clcomp)
par(mfrow = c(length(ccomp),2),mar=c(1,1,1,1))
for(i in seq_along(ccomp)){
ccompi <- ccomp[[i]]
clcompi <- clcomp[[i]]
barplot(ccompi[,2],names.arg = ccompi[,1],main = paste0('Sample',i,"'s C Composition"))
barplot(clcompi[,2],names.arg = clcompi[,1], main = paste0('Sample',i,"'s Cl Composition"))
}
})
output$results <- renderPrint({
li <- listsample()
pCl <- vapply(li,function(x) x$sumpCl,1)
rarea <- vapply(li,function(x) x$sumrarea,1)
if(input$log){
cons <- rarea/exp((pCl*input$slope+input$inc))
}else{
cons <- rarea/(pCl*input$slope+input$inc)
}
round(cons,2)
})
output$data <- renderDataTable({
sccp
})
})
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