"Añadido exportar figura"
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Costa
@@ -10,11 +10,9 @@ library(flextable)
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source("funcions.R")
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ui <- fluidPage(
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# Application title
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titlePanel("ELISPOTs"),
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sidebarLayout(
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#Navbar
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navbarPage("ELISPOTS",
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tabPanel("Diseño",
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sidebarPanel(
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fileInput(inputId = "file1", label = "Dades", multiple = F),
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selectInput(inputId = "test", "Test Estadístic", selected = "Ttest", choices = c("T-test (adj Holm)","Wilcoxon (adj Holm)")),
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@@ -28,7 +26,26 @@ ui <- fluidPage(
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plotOutput("distPlot"),
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uiOutput("flexstats")
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)
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),
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tabPanel("Exportar",
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sidebarPanel(width=2,
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sliderInput("width", "Ancho", min=1000, max=20000, step=1000, value=10000),
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sliderInput("height", "Altura", min=1000, max=20000, step=1000, value=6000),
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textInput("colors", label="Colors", value=""),
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sliderInput("boxplot-width", "% Ancho Boxplots", min=0.1, max=1, step=0.1, value=0.7),
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sliderInput("point-size", "Tamaño puntos", min=1, max=10, step=1, value=3),
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sliderInput("font-size", "Tamaño textos", min=5, max=30, step=1, value=11),
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checkboxInput(inputId = "stats2", label = "Mostrar estadística", value = F),
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checkboxInput(inputId = "legend", label = "Mostrar llegenda", value = T),
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selectInput("theme", "Seleccionar Tema", selected="BW", choices=c("BW", "Default", "Classic")),
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downloadButton("downloadPicture", "Exportar")
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),
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mainPanel(
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uiOutput("expPlotUI")
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)
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)
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)
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)
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# Define server logic required to draw a histogram
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@@ -36,6 +53,9 @@ server <- function(input, output) {
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dades<-reactiveValues()
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dades$taula<-NULL
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dades$stats<-NULL
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dades$final<-NULL
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dades$maps<-NULL
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dades$plot<-NULL
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observe({
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if (!is.null(input$file1)){
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dades$taula<-read_xlsx(input$file1$datapath)
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@@ -68,7 +88,6 @@ server <- function(input, output) {
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t_substr[,3:ncol(t_substr)]<-apply(t_substr[,3:ncol(t_substr)],2, function(x) replace(x, which(x < 0),0))
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colnames(t_substr)<-c("Mice", "Groups", colnames(t_mean)[2:ncol(t_mean)])
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}else{
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print(1)
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t_especifica<-t_mean[,grep("Mock_", colnames(t_mean), invert=T)]
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t_mock<-t_mean[,c(which(colnames(t_mean) == "Mice"),grep("Mock_", colnames(t_mean)))]
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t_temp<-melt(t_especifica, variable.name = "condition", value.name = "spots")
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@@ -97,6 +116,7 @@ server <- function(input, output) {
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t_maps[["brackets"]]<-as.data.frame(matrix(nrow = 0, ncol=4))
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colnames(t_maps$brackets)<-c("y1", "y2", "x1", "x2")
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dades$stats<<-t_stats
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dades$maps<<-t_maps
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}else{
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if (input$test == "T-test (adj Holm)"){
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t_stats<-multi_stats(t, "value", "variable", "Groups", stat.test = "ttest")
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@@ -109,8 +129,9 @@ server <- function(input, output) {
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t_stats<-t_stats %>% filter(p.signif != "ns")
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t_maps<-generate_labstats(t_stats, t, "value", "variable", "Groups")
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dades$maps<<-t_maps
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}
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dades$final<<-t_substr %>% select(-c(ctrl, mock))
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set.seed(123)
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if (input$positive == T){
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ggplot(melt(t_substr, id=c("Mice", ctrl, "Groups")), aes(variable, value))+
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@@ -162,6 +183,53 @@ server <- function(input, output) {
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}
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})
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output$expPlotUI<- renderUI({
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if (!is.null(dades$final)){
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plotOutput("expPlot", width=paste0(input$width/10,"px"), height = paste0(input$height/10, "px"))
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}
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})
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output$expPlot <- renderPlot({
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observeEvent(dades$final, {})
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if (!is.null(dades$final)){
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t_substr<-dades$final
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t_stats<-dades$stats %>% filter(p.signif != "ns")
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t_maps<-dades$maps
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ids<-c("Mice", "Groups")
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set.seed(123)
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g<-ggplot(melt(t_substr, id=ids), aes(variable, value))+
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labs(x="", y="Spots/2.5*10^5 cells")+
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geom_boxplot(color="black", aes(fill=Groups), alpha=0.4, outlier.alpha = 0, position=position_dodge(width=0.8),width=input$`boxplot-width`)+
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geom_jitter(position=position_jitterdodge(jitter.width = 0.2), shape=21, aes(fill=Groups), size=input$`point-size`)+
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scale_x_discrete(limits=colnames(t_substr)[!colnames(t_substr) %in% c("Mice", "Groups")])
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if (input$theme == "BW"){
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g<-g+theme_bw(base_size = input$`font-size`)
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}
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if (input$theme == "Classic"){
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g<-g+theme_classic(base_size = input$`font-size`)
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}
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if (input$theme == "Default"){
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g<-g+theme_gray(base_size = input$`font-size`)
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}
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g<-g+theme(axis.text.x=element_text(angle=45, hjust=1))
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if (input$stats2 == T){
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g<-g+geom_segment(data=t_maps$brackets, aes(x=x1, xend=x2, y=y1, yend=y2), color="black")+
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geom_text(data=t_stats, aes(t_maps$label$x, t_maps$label$y, label=p.signif), color="black")
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}
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if (input$legend == F){
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g<-g+guides(color=FALSE, fill=FALSE)
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}
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if (input$colors != ""){
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v_col<-strsplit(input$colors, ",")[[1]]
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g<-g+scale_color_manual(values=v_col)+
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scale_fill_manual(values=v_col)
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}
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dades$plot<<-g
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g
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}
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}, res=72)
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output$downloadData <- downloadHandler(
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filename = function() {
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paste("elispot", ".zip", sep="")
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@@ -179,6 +247,20 @@ server <- function(input, output) {
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},
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contentType="application/zip"
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)
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output$downloadPicture <- downloadHandler(
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filename = function() {
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paste("Figura", ".png", sep="")
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},
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content = function(file){
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print(file)
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# tempReport <- file.path(tempdir(), "elispots.Rmd")
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# file.copy("elispots.Rmd", tempReport, overwrite = TRUE)
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png(file, width = input$width, height=input$height, units = "px", res=720)
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plot(dades$plot)
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dev.off()
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}
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)
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}
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# Run the application
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