From ef45b35db7e047cae6fc2264af7aa5f0d17e5699 Mon Sep 17 00:00:00 2001 From: Costa <47926492N@ICO.SCS.local> Date: Wed, 11 Nov 2020 15:30:06 +0100 Subject: [PATCH] =?UTF-8?q?"A=C3=B1adido=20exportar=20figura"?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- app.R | 98 ++++++++++++++++++++++++++++++++++++++++++++++++++++++----- 1 file changed, 90 insertions(+), 8 deletions(-) diff --git a/app.R b/app.R index eacb523..21b8700 100644 --- a/app.R +++ b/app.R @@ -10,11 +10,9 @@ library(flextable) source("funcions.R") ui <- fluidPage( - - # Application title - titlePanel("ELISPOTs"), - - sidebarLayout( + #Navbar + navbarPage("ELISPOTS", + tabPanel("Diseño", sidebarPanel( fileInput(inputId = "file1", label = "Dades", multiple = F), selectInput(inputId = "test", "Test Estadístic", selected = "Ttest", choices = c("T-test (adj Holm)","Wilcoxon (adj Holm)")), @@ -28,7 +26,26 @@ ui <- fluidPage( plotOutput("distPlot"), uiOutput("flexstats") ) - ) + ), + tabPanel("Exportar", + sidebarPanel(width=2, + sliderInput("width", "Ancho", min=1000, max=20000, step=1000, value=10000), + sliderInput("height", "Altura", min=1000, max=20000, step=1000, value=6000), + textInput("colors", label="Colors", value=""), + sliderInput("boxplot-width", "% Ancho Boxplots", min=0.1, max=1, step=0.1, value=0.7), + sliderInput("point-size", "Tamaño puntos", min=1, max=10, step=1, value=3), + sliderInput("font-size", "Tamaño textos", min=5, max=30, step=1, value=11), + checkboxInput(inputId = "stats2", label = "Mostrar estadística", value = F), + checkboxInput(inputId = "legend", label = "Mostrar llegenda", value = T), + selectInput("theme", "Seleccionar Tema", selected="BW", choices=c("BW", "Default", "Classic")), + downloadButton("downloadPicture", "Exportar") + ), + mainPanel( + uiOutput("expPlotUI") + ) + ) + ) + ) # Define server logic required to draw a histogram @@ -36,6 +53,9 @@ server <- function(input, output) { dades<-reactiveValues() dades$taula<-NULL dades$stats<-NULL + dades$final<-NULL + dades$maps<-NULL + dades$plot<-NULL observe({ if (!is.null(input$file1)){ dades$taula<-read_xlsx(input$file1$datapath) @@ -68,7 +88,6 @@ server <- function(input, output) { t_substr[,3:ncol(t_substr)]<-apply(t_substr[,3:ncol(t_substr)],2, function(x) replace(x, which(x < 0),0)) colnames(t_substr)<-c("Mice", "Groups", colnames(t_mean)[2:ncol(t_mean)]) }else{ - print(1) t_especifica<-t_mean[,grep("Mock_", colnames(t_mean), invert=T)] t_mock<-t_mean[,c(which(colnames(t_mean) == "Mice"),grep("Mock_", colnames(t_mean)))] t_temp<-melt(t_especifica, variable.name = "condition", value.name = "spots") @@ -97,6 +116,7 @@ server <- function(input, output) { t_maps[["brackets"]]<-as.data.frame(matrix(nrow = 0, ncol=4)) colnames(t_maps$brackets)<-c("y1", "y2", "x1", "x2") dades$stats<<-t_stats + dades$maps<<-t_maps }else{ if (input$test == "T-test (adj Holm)"){ t_stats<-multi_stats(t, "value", "variable", "Groups", stat.test = "ttest") @@ -109,8 +129,9 @@ server <- function(input, output) { t_stats<-t_stats %>% filter(p.signif != "ns") t_maps<-generate_labstats(t_stats, t, "value", "variable", "Groups") + dades$maps<<-t_maps } - + dades$final<<-t_substr %>% select(-c(ctrl, mock)) set.seed(123) if (input$positive == T){ ggplot(melt(t_substr, id=c("Mice", ctrl, "Groups")), aes(variable, value))+ @@ -162,6 +183,53 @@ server <- function(input, output) { } }) + output$expPlotUI<- renderUI({ + if (!is.null(dades$final)){ + plotOutput("expPlot", width=paste0(input$width/10,"px"), height = paste0(input$height/10, "px")) + } + }) + + output$expPlot <- renderPlot({ + observeEvent(dades$final, {}) + if (!is.null(dades$final)){ + t_substr<-dades$final + t_stats<-dades$stats %>% filter(p.signif != "ns") + t_maps<-dades$maps + + ids<-c("Mice", "Groups") + set.seed(123) + g<-ggplot(melt(t_substr, id=ids), aes(variable, value))+ + labs(x="", y="Spots/2.5*10^5 cells")+ + geom_boxplot(color="black", aes(fill=Groups), alpha=0.4, outlier.alpha = 0, position=position_dodge(width=0.8),width=input$`boxplot-width`)+ + geom_jitter(position=position_jitterdodge(jitter.width = 0.2), shape=21, aes(fill=Groups), size=input$`point-size`)+ + scale_x_discrete(limits=colnames(t_substr)[!colnames(t_substr) %in% c("Mice", "Groups")]) + if (input$theme == "BW"){ + g<-g+theme_bw(base_size = input$`font-size`) + } + if (input$theme == "Classic"){ + g<-g+theme_classic(base_size = input$`font-size`) + } + if (input$theme == "Default"){ + g<-g+theme_gray(base_size = input$`font-size`) + } + g<-g+theme(axis.text.x=element_text(angle=45, hjust=1)) + if (input$stats2 == T){ + g<-g+geom_segment(data=t_maps$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") + } + if (input$legend == F){ + g<-g+guides(color=FALSE, fill=FALSE) + } + if (input$colors != ""){ + v_col<-strsplit(input$colors, ",")[[1]] + g<-g+scale_color_manual(values=v_col)+ + scale_fill_manual(values=v_col) + } + dades$plot<<-g + g + } + }, res=72) + output$downloadData <- downloadHandler( filename = function() { paste("elispot", ".zip", sep="") @@ -179,6 +247,20 @@ server <- function(input, output) { }, contentType="application/zip" ) + output$downloadPicture <- downloadHandler( + filename = function() { + paste("Figura", ".png", sep="") + }, + content = function(file){ + print(file) + # tempReport <- file.path(tempdir(), "elispots.Rmd") + # file.copy("elispots.Rmd", tempReport, overwrite = TRUE) + png(file, width = input$width, height=input$height, units = "px", res=720) + plot(dades$plot) + dev.off() + + } + ) } # Run the application