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server.R
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server.R
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pkgTest <- function(x)
{
if (!require(x,character.only = TRUE))
{
install.packages(x,dep=TRUE)
if(!require(x,character.only = TRUE)) stop("Package not found")
}
}
pkgTest("shiny")
pkgTest("ggplot2")
pkgTest("xtable")
AbBkSCol <- c("springgreen4", "cornflowerblue", "mediumvioletred", "darkorange", "red4", "plum3", "wheat3", "orangered2", "blue4")
shinyServer(function(input, output) {
data.set <- reactive({
Seed.Dat <- read.csv("all-najust3 + MET.csv", stringsAsFactors=FALSE)
Seed.Dat$Sowing <- as.character(Seed.Dat$Sowing)
if( input$Sowz != "All") {
Seed.Dat <- Seed.Dat[Seed.Dat$Sowing == input$Sowz, ]
}
if(input$Filmz != "All") {
Seed.Dat <- Seed.Dat[Seed.Dat$Treatment == input$Filmz, ]
}
if(input$Primez != "All") {
Seed.Dat <- Seed.Dat[Seed.Dat$P.NP == input$Primez, ]
}
if(input$Lociz != "All") {
Seed.Dat <- Seed.Dat[Seed.Dat$Location == input$Lociz, ]
}
if(input$Yearz != "All") {
Seed.Dat <- Seed.Dat[Seed.Dat$Year == input$Yearz, ]
}
sub <- substring(text = input$name, first = 1, last = (nchar(input$name)-4))
Seed.Dat <- Seed.Dat
})
output$text <- renderUI({
if(input$ratio) {
if(input$Yearz != "All") {stop('In order to compere the years you must enter All in the years selection field')}
X <- data.set()
X[is.na(X)] <- 0
fst <- X[X$Year == '2013 Dat', ]
fst <- fst[order(fst$P.NP, fst$Treatment, fst$Sowing, fst$Location, fst$PLOT),]
last <- fst
snd <- X[X$Year == '2014 Dat', ]
snd <- snd[order(snd$P.NP, snd$Treatment, snd$Sowing, snd$Location, snd$PLOT),]
if(nrow(fst) != nrow(snd)) {stop('The to sets of data are not the same length, And must be!')}
for(i in seq(1, nrow(fst), 1)) {
last$'No.Plants.est'[i] <- snd$'No.Plants.est'[i] - fst$'No.Plants.est'[i]
}
xopt <- unique(last[,input$x])
text.norm <- paste("Not/Normal distribution")
if(input$x != "Sowing") {
for(Nor in xopt) {
isNorm <- shapiro.test(x = last[,input$y][last[,input$x] == Nor])
text.norm <- paste(text.norm, "<br/><b>", Nor, "</b> is ", if(isNorm$p.value >= 0.05) {"<font color=#385737> Normally Distributed </font color=#385737>"}else {"<font color=#902277><b> Not Normally Distributed </b></font color=#902277>"})
}
if(isNorm$p.value >= 0.05) {ttest <- t.test(x = last[,input$y][last[,input$x] == xopt[1]], y = last[,input$y][last[,input$x] == xopt[2]])
text.test <- paste("T Test P value = ", round(ttest$p.value, digits = 3), " - Result is", if(ttest$p.value >= 0.05) {"<font color=#111111> Not Significantly Different </font color=#111111>"}else {"<font color=#ff2f82><b> Significantly Different </b></font color=#ff2f82>"} )
}else {npwill <- wilcox.test(last[,input$y][last[,input$x] == xopt[1]], last[,input$y][last[,input$x] == xopt[2]])
text.test <- paste("Wilcox Test P value = ", round(npwill$p.value, digits = 3), " - Result is", if(npwill$p.value >= 0.05) {"<font color=#111111> Not Significantly Different </font color=#111111>"}else {"<font color=#ff2f82><b> Significantly Different </b></font color=#ff2f82>"} )
}
}
#Anno <- aov(last[,input$y] ~ as.factor(last[,input$x]))
Npanno <- kruskal.test(last[,input$y]~as.factor(last[,input$x]))
#print(summary(Anno))
#print(TukeyHSD(Anno, conf.level = 0.95))
#print(pairwise.t.test(last[,input$y], last[,input$x], p.adjust="bonferroni"))
text.k <- paste("Kruskal-Wallis Test P value = ", round(Npanno$p.value, digits = 3), " - Result is", if(Npanno$p.value >= 0.05) {"<font color=#111111> Not Significantly Different </font color=#111111>"}else {"<font color=#ff2f82><b> Significantly Different </b></font color=#ff2f82>"} )
if(Npanno$p.value <= 0.05) {
posthoc <- pairwise.wilcox.test(last[,input$y], last[,input$x], p.adj="bonferroni", exact=F)
posthoc <- as.matrix(posthoc$p.value)
posthock <- ifelse(posthoc <= 0.05, paste("<font color=#ff2f82>",round(posthoc, 3), "</font>"), paste("<font color=#051153>",round(posthoc, 3), "</font>"))
print("* denotes some significance see aboth for values")
#posthock <- xtable(posthock)
posthock <- print.xtable(xtable(posthock,digits=4), type="html",sanitize.text.function=function(x){x}, html.table.attributes='border=5 align=center width=500')
#print(posthock, type = "html", html.table.attributes='border=5 align=center width=500' )
texttest <- paste("<p style=font-size:12px><font color=#952c1e><i> See below output for post hoc pairwise wilcox test p values</i></font color=#952c1e></p style=font-size:12px><br/>", posthock)
NormNorm <- 100;
}
}else {
All <- data.set()
xopt <- unique(All[,input$x])
text.norm <- paste("Not/Normal distribution")
NormNorm <- 0;
if(input$x != "Sowing") {
for(Nor in xopt) {
isNorm <- shapiro.test(x = All[,input$y][All[,input$x] == Nor])
text.norm <- paste(text.norm, "<br/><b>", Nor, "</b> is ", if(isNorm$p.value >= 0.05) {"<font color=#385737> Normally Distributed </font color=#385737>"}else {"<font color=#902277><b> Not Normally Distributed </b></font color=#902277>"})
NormNorm <- isNorm$p.value + NormNorm
}
if(NormNorm/length(xopt) >= 0.05) {ttest <- t.test(x = All[,input$y][All[,input$x] == xopt[1]], y = All[,input$y][All[,input$x] == xopt[2]])
text.test <- paste("T Test P value = ", round(ttest$p.value, digits = 4), " - Result is", if(ttest$p.value >= 0.05) {"<font color=#111111> Not Significantly Different </font color=#111111>"}else {"<font color=#ff2f82><b> Significantly Different </b></font color=#ff2f82>"} )
}else {npwill <- wilcox.test(All[,input$y][All[,input$x] == xopt[1]], All[,input$y][All[,input$x] == xopt[2]])
text.test <- paste("Wilcox Test P value = ", round(npwill$p.value, digits = 4), " - Result is", if(npwill$p.value >= 0.05) {"<font color=#111111> Not Significantly Different </font color=#111111>"}else {"<font color=#ff2f82><b> Significantly Different </b></font color=#ff2f82>"} )
}
} else {
#Anno <- aov(All[,input$y] ~ as.factor(All[,input$x]))
Npanno <- kruskal.test(All[,input$y]~as.factor(All[,input$x]))
#print(summary(Anno))
#print(TukeyHSD(Anno, conf.level = 0.95))
#print(pairwise.t.test(All[,input$y], All[,input$x], p.adjust="bonferroni"))
text.k <- paste("Kruskal-Wallis Test P value = ", round(Npanno$p.value, digits = 4), " - Result is", if(Npanno$p.value >= 0.05) {"<font color=#111111> Not Significantly Different </font color=#111111>"}else {"<font color=#ff2f82><b> Significantly Different </b></font color=#ff2f82>"} )
if(Npanno$p.value <= 0.05) {
posthoc <- pairwise.wilcox.test(All[,input$y], All[,input$x], p.adj="bonferroni", exact=F)
posthoc <- as.matrix(posthoc$p.value)
posthock <- ifelse(posthoc <= 0.05, paste("<font color=#ff2f82>",round(posthoc, 3), "</font>"), paste("<font color=#051153>",round(posthoc, 3), "</font>"))
print("* denotes some significance see aboth for values")
#posthock <- xtable(posthock)
posthock <- print.xtable(xtable(posthock,digits=4), type="html",sanitize.text.function=function(x){x}, html.table.attributes='border=5 align=center width=500')
#print(posthock, type = "html", html.table.attributes='border=5 align=center width=500' )
texttest <- paste("<p style=font-size:12px><font color=#952c1e><i> See below output for post hoc pairwise wilcox test p values</i></font color=#952c1e></p style=font-size:12px><br/>", posthock)
NormNorm <- 100;
}
}
}
disclamer <- "<p style=font-size:9px><font color=#ff5737>Theas stats are only a indication and should probably be checked outside of an automated script</p style=font-size:9px></font color=#ff5737>"
HTML(paste(text.norm, "-", if(input$x != "Sowing") {text.test} else {text.k}, if(NormNorm == 100) {texttest}, disclamer, sep = '<br/>'))
})
output$plot <- renderPlot({
if(input$ratio) {
if(input$Yearz != "All") {stop('In order to compere the years you must enter All in the years selection field')}
X <- data.set()
X[is.na(X)] <- 0
fst <- X[X$Year == '2013 Dat', ]
fst <- fst[order(fst$P.NP, fst$Treatment, fst$Sowing, fst$Location, fst$PLOT),]
last <- fst
snd <- X[X$Year == '2014 Dat', ]
snd <- snd[order(snd$P.NP, snd$Treatment, snd$Sowing, snd$Location, snd$PLOT),]
if(nrow(fst) != nrow(snd)) {stop('The to sets of data are not the same length, And must be!')}
for(i in seq(1, nrow(fst), 1)) {
last$'No.Plants.est'[i] <- snd$'No.Plants.est'[i] - fst$'No.Plants.est'[i]
}
p <- ggplot(last, aes_string(x=input$x, y=input$y)) + scale_colour_manual(values=AbBkSCol)
}else {
p <- ggplot(data.set(), aes_string(x=input$x, y=input$y)) + scale_colour_manual(values=AbBkSCol)
}
if (input$boxplot)
p <- p + geom_boxplot()
if (input$color != 'X Value') {
p <- p + aes_string(color=input$color)
} else {
p <- p + aes_string(color=input$x)
}
if(input$viol)
p <- p + geom_violin(position = "dodge")
if (input$points)
p <- p + geom_point() + geom_jitter()
################# use this to set the y axis
#p <- p + ylim(0,60)
#################
print(p)
}, height=700)
observe({
if (input$ChangeDir == 0) {
write(getwd(), "Dir")
return()
}
isolate({
Dir <- choose.dir("C://", "Input Destination Folder")
print(Dir)
if(is.na(Dir)) {
write(getwd(), "Dir")
}else {
write(Dir, "Dir")
}
})
})
TheDir <- reactive({
input$ChangeDir
Dir <- read.table("Dir", sep = "&")
Dir <- as.character(Dir[1,1])
Dir
})
output$DIR <- renderText({
Dir <- paste(TheDir(), "/", sep = "")
Dir
})
observe({
Name <- paste(input$x, " by ", input$y,
if(input$color != "X Value") {paste(" color-", input$color, sep = "")},
"_", if(input$Sowz != "All") {paste(" sowing-", input$Sowz, "_", sep = "")},
if(input$Filmz != "All") {paste(" film-", input$Filmz, "_", sep = "")},
if(input$Primez != "All") {paste(" priming-", input$Primez, "_", sep = "")},
if(input$Lociz != "All") {paste(" in-", input$Lociz, "_", sep = "")},
if(input$Yearz != "All") {paste(" in-", input$Yearz, "_", sep = "")},
input$ExtraName, ".", input$ext,sep = "")
print(Name)
if(file.exists(Name)) {
print("OverWrite!?")
}
write(Name, "FileName")
})
IdealName <- reactive({
input$Sowz;input$Filmz;input$Primez;input$Lociz;input$ExtraName;input$Yearz;input$x;input$y;input$color;input$ext;
IdealName <- read.table("FileName", sep = "&")
IdealName <- as.character(IdealName[1,1])
IdealName
})
output$Name <- renderUI({
Name <- HTML(paste("<font color=#b71e66> <b> ", IdealName(), " </b> </font color=#b71e66><br/>",sep = ""))
})
observe({
if (input$save == 0)
return()
isolate({
ggsave(paste(TheDir(), "/", IdealName(), sep = ""), dpi = 500)
# if(input$csv){
# write.csv(paste(sub, ".csv", sep = ""), data.set())
# }
})
})
})