|
|
- library(shiny)
- library(openxlsx)
- library(readxl)
- library(ggplot2)
- library(reshape2)
- library(dplyr)
- library(ggbeeswarm)
- library(magrittr)
- library(flextable)
- source("funcions.R")
-
- ui <- fluidPage(
-
- # Application title
- titlePanel("ELISPOTs"),
-
- sidebarLayout(
- sidebarPanel(
- fileInput(inputId = "file1", label = "Dades", multiple = F),
- selectInput(inputId = "test", "Test Estadístic", selected = "Ttest", choices = c("T-test (adj Holm)","Wilcoxon (adj Holm)")),
- sliderInput(inputId = "umbral_pos", "Mínimo para positivo:", min = 0, max=100, step = 5, value = 10),
- checkboxInput(inputId = "positive", label = "Mostrar positivitat", value = F),
- checkboxInput(inputId = "showstats", label = "Mostrar estadística", value = F),
- downloadButton("downloadData", "Descarregar Informe")
- ),
-
- mainPanel(
- plotOutput("distPlot"),
- uiOutput("flexstats")
- )
- )
- )
-
- # Define server logic required to draw a histogram
- server <- function(input, output) {
- dades<-reactiveValues()
- dades$taula<-NULL
- dades$stats<-NULL
- observe({
- if (!is.null(input$file1)){
- dades$taula<-read_xlsx(input$file1$datapath)
- }
- })
-
- output$distPlot <- renderPlot({
- observeEvent(dades$taula, {})
- if (!is.null(dades$taula)){
-
- ctrl<-"Ctrl+"
- mock<-"Mock"
-
- table<-dades$taula[,colnames(dades$taula) != "Groups"]
- t_mean<-dcast(melt(table, id="Mice"),Mice~variable, mean, na.rm=T)
-
- t_substr<-data.frame("Mice"=t_mean[,1],
- as.data.frame(t(apply(t_mean[,2:ncol(table)], 1, function(x) x-x[mock])))
- )
- t_mean_group<-merge(t_mean, unique(dades$taula[c("Mice","Groups")]), id="Mice")
- mock_mean<-dcast(t_mean_group, Groups~., value.var=mock, mean)
- mock_mean[,2]<-mock_mean[,2]*2
- mock_mean[mock_mean$. < input$umbral_pos,2]<-input$umbral_pos
-
- t_substr<-merge(t_substr, unique(dades$taula[c("Mice","Groups")]), id="Mice")
- t_substr<-t_substr[,c(1, ncol(t_substr), 2:(ncol(t_substr)-1))]
- t_substr<-t_substr[,c("Mice", "Groups", colnames(t_substr)[!colnames(t_substr) %in% c("Mice", "Groups")])]
- t_substr[,3:ncol(t_substr)]<-apply(t_substr[,3:ncol(t_substr)],2, function(x) replace(x, which(x < 0),0))
- colnames(t_substr)<-c("Mice", "Groups", colnames(t_mean)[2:ncol(t_mean)])
-
- t_substr_gp<-t_substr
- t_substr_gp[3:ncol(t_substr)]<-apply(t_substr[3:ncol(t_substr)], 2, function(x) gsub(".",",",x, fixed=T))
- t_substr_gp<-t_substr_gp[order(factor(t_substr_gp$Mice, levels = unique(table$Mice))),]
- doc<-t(t_substr_gp)
-
- write.xlsx(doc, "data4graphpad.xlsx",rowNames=T)
-
- t<-melt(t_substr[,!colnames(t_substr) %in% c(ctrl, mock)])
- if (input$test == "T-test (adj Holm)"){
- t_stats<-multi_stats(t, "value", "variable", "Groups", stat.test = "ttest")
- }
- if (input$test == "Wilcoxon (adj Holm)"){
- t_stats<-multi_stats(t, "value", "variable", "Groups", stat.test = "wilcox")
- }
-
- dades$stats<<-t_stats
- t_stats<-t_stats %>% filter(p.signif != "ns")
-
- t_maps<-generate_labstats(t_stats, t, "value", "variable", "Groups")
-
- if (input$showstats == F){
- t_stats<-as.data.frame(matrix(nrow=0, ncol=6))
- colnames(t_stats)<-c("variable", "group1", "group2", "p.adj", "p.signif", "Method")
- t_maps<-list()
- t_maps[["label"]]<-as.data.frame(matrix(nrow = 0, ncol=2))
- colnames(t_maps$label)<-c("x", "y")
- t_maps[["brackets"]]<-as.data.frame(matrix(nrow = 0, ncol=4))
- colnames(t_maps$brackets)<-c("y1", "y2", "x1", "x2")
- }
-
- set.seed(123)
- if (input$positive == T){
- ggplot(melt(t_substr, id=c("Mice", ctrl, "Groups")), aes(variable, value))+
- labs(x="", y="Spots/2.5*10^5 cells")+
- # geom_errorbar(stat="summary", position=position_dodge(width=0.9), width=0.5, aes(fill=Groups))+
- geom_hline(data=mock_mean, aes(color=Groups, yintercept = `.`))+
- # geom_bar(stat="summary", position="dodge", color="black", aes(fill=Groups))+
- geom_boxplot(color="black", aes(fill=Groups), alpha=0.4, outlier.alpha = 0)+
- geom_jitter(position=position_jitterdodge(jitter.width = 0.2), shape=21, aes(fill=Groups), size=3)+
- # geom_quasirandom(position = position_quasirandom(), shape=21)+
- scale_x_discrete(limits=colnames(t_substr)[!colnames(t_substr) %in% c("Mice", "Groups", ctrl, mock)])+
- geom_segment(data=t_maps$brackets, aes(x=x1, xend=x2, y=y1, yend=y2), color="black")+
- geom_text(data=t_stats, aes(t_maps$label$x, t_maps$label$y, label=p.signif), color="black")+
- theme_bw()+
- theme(axis.text.x=element_text(angle=45, hjust=1))
- }else{
- ggplot(melt(t_substr, id=c("Mice", ctrl, "Groups")), aes(variable, value))+
- labs(x="", y="Spots/2.5*10^5 cells")+
- # geom_errorbar(stat="summary", position=position_dodge(width=0.9), width=0.5, aes(fill=Groups))+
- # geom_bar(stat="summary", position="dodge", color="black", aes(fill=Groups))+
- geom_boxplot(color="black", aes(fill=Groups), alpha=0.4, outlier.alpha = 0)+
- geom_jitter(position=position_jitterdodge(jitter.width = 0.2), shape=21, aes(fill=Groups), size=3)+
- # geom_quasirandom(width=0.2, position=position_dodge(), shape=21)+
- scale_x_discrete(limits=colnames(t_substr)[!colnames(t_substr) %in% c("Mice", "Groups", ctrl, mock)])+
- geom_segment(data=t_maps$brackets, aes(x=x1, xend=x2, y=y1, yend=y2), color="black")+
- geom_text(data=t_stats, aes(t_maps$label$x, t_maps$label$y, label=p.signif), color="black")+
- theme_bw()+
- theme(axis.text.x=element_text(angle=45, hjust=1))
- }
- }
-
- })
-
- output$flexstats <- renderUI({
- observeEvent(dades$stats, {})
- t_stats<-dades$stats
- if (!is.null(dades$stats)){
- return(
- t_stats %>%
- flextable() %>%
- theme_vanilla() %>%
- fontsize(size=14, part="all") %>%
- padding(padding=10, part="all") %>%
- color(~ p.adj < 0.05, color = "red")%>%
- autofit()
- ) %>%
- htmltools_value()
- }
- })
-
- output$downloadData <- downloadHandler(
- filename = function() {
- paste("elispot", ".zip", sep="")
- },
- content = function(file){
- print(file)
- # tempReport <- file.path(tempdir(), "elispots.Rmd")
- # file.copy("elispots.Rmd", tempReport, overwrite = TRUE)
- params=list(file=input$file1$datapath, positive=input$positive, showstats=input$showstats, test=input$test, umbral_pos=input$umbral_pos)
- rmarkdown::render("elispots.Rmd", output_file="Results_elispot.html", params=params, envir = new.env(parent = globalenv()))
- zip(file,
- c("Results_elispot.html","data4graphpad.xlsx")
- )
-
- },
- contentType="application/zip"
- )
- }
-
- # Run the application
- shinyApp(ui = ui, server = server)
|
