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@ -5,6 +5,13 @@ library(reshape2) |
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library(Matrix) |
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library(Matrix) |
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library(CitFuns) |
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library(CitFuns) |
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library(BDCIT) |
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library(BDCIT) |
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library(openCyto) |
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library(flowCore) |
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library(flowWorkspace) |
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library(CytoML) |
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library(ggcyto) |
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filter<-dplyr::filter |
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print(getwd()) |
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print(getwd()) |
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source("../sqlFunctions.R", encoding = "UTF-8") |
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source("../sqlFunctions.R", encoding = "UTF-8") |
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@ -19,6 +26,8 @@ rna<-data.frame("UMID"="","UM"="") |
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sqlInitialize(ruta="../ruta_database.R") |
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sqlInitialize(ruta="../ruta_database.R") |
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# UI ---- |
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ui <- fluidPage( |
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ui <- fluidPage( |
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# Application title |
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# Application title |
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@ -27,6 +36,8 @@ ui <- fluidPage( |
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#sidebarLayout( |
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#sidebarLayout( |
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#Navbar |
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#Navbar |
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navbarPage("BDAccess", |
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navbarPage("BDAccess", |
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## Update ---- |
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tabPanel("Update", |
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tabPanel("Update", |
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sidebarPanel( |
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sidebarPanel( |
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selectInput("dbtype", "", selected="UM", choices=c("UM", "OV","CC")), |
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selectInput("dbtype", "", selected="UM", choices=c("UM", "OV","CC")), |
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@ -52,6 +63,8 @@ ui <- fluidPage( |
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) |
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) |
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) |
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) |
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), |
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), |
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## Visor ---- |
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tabPanel("Visor", |
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tabPanel("Visor", |
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sidebarPanel( |
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sidebarPanel( |
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radioButtons("nhc", label = h3("Código"), |
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radioButtons("nhc", label = h3("Código"), |
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@ -63,9 +76,35 @@ ui <- fluidPage( |
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mainPanel( |
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mainPanel( |
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htmlOutput("report"), |
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htmlOutput("report"), |
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h3("Nitrogen"), |
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h3("Nitrogen"), |
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tableOutput("nitrogen") |
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tableOutput("nitrogen"), |
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plotOutput("visorplot", height = "1000px") |
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) |
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) |
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), |
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), |
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## Citometría ---- |
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tabPanel("Citometría", |
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sidebarPanel( |
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selectInput("phenotype", "Tipo de análisis", selected="Pop", choices=c("Pop", "IC")), |
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), |
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mainPanel( |
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tabsetPanel( |
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tabPanel("Entrada", |
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actionButton("goButtonDir","Selecciona directorio fenotipo"), |
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textOutput("session"), |
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hr(), |
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actionButton("fcsconvert", "Convertir a fcs"), |
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hr(), |
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actionButton("pngexport", "Exportar informes"), |
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actionButton("popexport", "Actualizar BBDD") |
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), |
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tabPanel("Visor", |
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) |
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) |
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) |
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), |
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## scRNAseq ---- |
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tabPanel("scRNAseq", |
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tabPanel("scRNAseq", |
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sidebarPanel( |
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sidebarPanel( |
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textInput("sqlquery", label = "sqlquery", value = ""), |
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textInput("sqlquery", label = "sqlquery", value = ""), |
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@ -87,10 +126,11 @@ ui <- fluidPage( |
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) |
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# Define server logic required to draw a histogram |
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# Define server logic required to draw a histogram |
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# Server ---- |
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server <- function(input, output) { |
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server <- function(input, output) { |
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## Update |
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## Update ---- |
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values <- reactiveValues() |
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values <- reactiveValues() |
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values[["DF"]]<-DF |
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values[["DF"]]<-DF |
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values[["samples"]]<-samples |
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values[["samples"]]<-samples |
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@ -618,8 +658,9 @@ server <- function(input, output) { |
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} |
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} |
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}) |
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}) |
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## Visor |
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## Visor ---- |
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output$report<-renderUI({ |
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output$report<-renderUI({ |
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samples<-sqlFetch(dta, "samples") |
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samples<-sqlFetch(dta, "samples") |
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if (input$nhc == 1){samples_sel<-samples %>% filter(OVID == input$id)} |
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if (input$nhc == 1){samples_sel<-samples %>% filter(OVID == input$id)} |
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@ -786,8 +827,206 @@ server <- function(input, output) { |
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}) |
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}) |
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## scRNAseq |
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output$visorplot<-renderPlot({ |
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if (input$nhc == 3){ |
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pops<-sqlFetch(dta, "POPULATIONS") |
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g_pop<-pops %>% dplyr::filter(samples == input$id) %>% gather(pop,value,-samples) %>% |
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mutate(pop=factor(pop, levels=c("CD45pos_Alive","T_cells","CD8","CD4","DN","NK", "B_cells", |
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"CD45neg_LDneg","EpCAMneg_HLAIneg","EpCAMneg_HLAIpos","EpCAMpos_HLAIpos"))) %>% |
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ggplot(aes(pop, value))+ |
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geom_bar(stat="identity", color="black", fill="grey70")+ |
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labs(title = input$id, y="% parent", x="")+ |
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theme_bw()+ |
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theme(axis.text.x = element_text(angle=90, hjust=1, vjust=0.5)) |
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tl<-sqlFetch(dta, "IC") %>% filter(samples == input$id) |
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mtl<-melt(tl, variable.name = "Receptors") |
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mtl$Receptors<-as.character(mtl$Receptors) #Para poder depurar bien el texto, lo pasamos a tipo character |
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mtl$Receptors<-gsub("n","-",mtl$Receptors, fixed = T) |
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mtl$Receptors<-gsub("p","+",mtl$Receptors, fixed = T) |
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mtl$Receptors<-gsub("_"," ",mtl$Receptors) |
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mtl[mtl$value < 1, "Receptors"]<-"Other" |
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mtl$Receptors<-gsub("[A-Z]*-*[0-9T]- *", "", mtl$Receptors) |
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mtl$Receptors<-gsub("+ $", "", mtl$Receptors) |
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mtl$Receptors[mtl$Receptors == ""]<-"All Negative" |
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mtl$Receptors<-factor(mtl$Receptors) |
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mtl$Population<-factor(mtl$Population, levels = c("CD8", "CD4")) |
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# colorCount<-length(unique(mtl$Receptors)) |
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# getPalette = colorRampPalette(RColorBrewer::brewer.pal(12, "Set3")) |
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color<-c(c("CTLA4+ LAG3+ PD1+ TIGIT+ TIM3+"="black","All Negative"="white","Other"="grey50", "PD1+"="#C07AFF", "CTLA4+"="#3EB3DE","TIM3+"="#5EF551","LAG3+"="#DEBB3E","TIGIT+"="#FA7055"), |
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c("CTLA4+ PD1+"="#6666FF","PD1+ TIM3+"="#849CA8", "LAG3+ PD1+"="#C47F9F","PD1+ TIGIT+"="#D259AA", "CTLA4+ TIM3+"="#4ED498", "CTLA4+ LAG3+"="#8EB78E", "CTLA4+ TIGIT+"="#9C929A", "LAG3+ TIM3+"="#9ED848", "TIGIT+ TIM3+"="#ACB353", "LAG3+ TIGIT+"="#EC964A"), |
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c("CTLA4+ PD1+ TIGIT+"="#B86B6A","CTLA4+ PD1+ TIGIT+ TIM3+"="#B81515","LAG3+ PD1+ TIGIT+"="#007D8A", "PD1+ TIGIT+ TIM3+"="#D64545", "LAG3+ PD1+ TIGIT+ TIM3+"="#0f5860", "LAG3+ TIGIT+ TIM3+"="#50cad3")) |
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g_IC<-ggplot(mtl, aes(samples, value, fill=Receptors))+ |
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geom_bar(stat="summary", fun="sum",color="black")+ |
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labs(x="Patient", y="% CD8+", fill="")+ |
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facet_grid(.~Population)+ |
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scale_fill_manual(values = color[levels(mtl$Receptors)[levels(mtl$Receptors) %in% unique(mtl$Receptors)]])+ |
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theme_bw()+ |
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theme(axis.text.x=element_text(angle=45, hjust=1)) |
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ggpubr::ggarrange(g_pop, g_IC, heights = c(0.4, 0.6), ncol = 1) |
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} |
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}) |
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## Citometría ---- |
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observe({ |
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if(input$goButtonDir > 0){ |
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cito_dir<<-choose.dir() %>% gsub("\\","/",. ,fixed=T) %>% paste0("/") |
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output$session <- renderText( |
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cito_dir |
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) |
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} |
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}) |
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observeEvent(input$fcsconvert,{ |
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route<-cito_dir |
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files<-list.files(route, ".LMD") |
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for (lmd in files){ |
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fcs<-read.FCS(paste0(route,lmd), dataset = 2) |
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# fcs@parameters$desc<-c("FS-A","SS-A", paste("FL",1:10,"-A", sep = ""), "TIME") |
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# fcs@parameters$desc<-c("FS-H","FS-A","FS-W","SS-H","SS-A","TIME", paste("FL",1:10,"-A", sep = "")) |
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keyword(fcs)['$FIL']<-paste0(gsub(".LMD","",lmd), ".fcs") |
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write.FCS(fcs, paste0(route, gsub(".LMD","",lmd), ".fcs")) |
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} |
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}) |
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observeEvent(input$pngexport,{ |
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if (input$phenotype == "Pop"){ |
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route<-cito_dir |
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ws<-open_flowjo_xml(paste0(route,"Populations.wsp")) |
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gs<-flowjo_to_gatingset(ws, name="All Samples") |
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sampleNames(gs)<-sapply(sampleNames(gs), function(x) strsplit(x, "Pop ")[[1]][2]) %>% |
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gsub("[[:space:]][0-9]*.fcs_.[0-9]*","", . , perl = T) |
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for (samp in sampleNames(gs)){ |
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print(samp) |
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p<-autoplot(gs[[samp]], bins=64) |
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ggsave(paste0(route, samp,".pop.png"),p,width = 10, height = 10) |
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} |
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} |
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if (input$phenotype == "IC"){ |
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route<-cito_dir |
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ws<-open_flowjo_xml(paste0(route,"IC.wsp")) |
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gs<-flowjo_to_gatingset(ws, name="All Samples") |
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sampleNames(gs)<-sapply(sampleNames(gs), function(x) strsplit(x, "ICs ")[[1]][2]) %>% |
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gsub("[[:space:]][0-9]*.fcs_.[0-9]*","", . , perl = T) |
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names<-sampleNames(gs) %>% gsub("ab|Ab|AB|iso|Iso|ISO| ","",.) %>% unique() |
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nodes<-gs_get_pop_paths(gs) |
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nodes_parent<-nodes[!grepl("CTLA4|LAG3|PD1|TIGIT|TIM3|root$", nodes)] |
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nodes_cd4<-nodes[grepl("CTLA4$|LAG3$|PD1$|TIGIT$|TIM3$", nodes) & grepl("/CD4/",nodes)] |
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nodes_cd8<-nodes[grepl("CTLA4$|LAG3$|PD1$|TIGIT$|TIM3$", nodes) & grepl("/CD8/",nodes)] |
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for (id in names){ |
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print(id) |
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iso<-sampleNames(gs)[grepl(id, sampleNames(gs)) & grepl("iso",sampleNames(gs))] |
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ab<-sampleNames(gs)[grepl(id, sampleNames(gs)) & grepl("ab",sampleNames(gs))] |
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g1<-ggcyto_arrange(autoplot(gs[[ab]], nodes_parent, bins=128), nrow=1) |
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g2<-ggcyto_arrange(autoplot(gs[[iso]], nodes_cd8, bins=64), nrow=1) |
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g3<-ggcyto_arrange(autoplot(gs[[ab]], nodes_cd8, bins=64), nrow=1) |
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g4<-ggcyto_arrange(autoplot(gs[[iso]], nodes_cd4, bins=64), nrow=1) |
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g5<-ggcyto_arrange(autoplot(gs[[ab]], nodes_cd4, bins=64), nrow=1) |
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g_all<-gridExtra::gtable_rbind(g1,g2,g3,g4,g5) |
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ggsave(paste0(route,id,".IC.png"), g_all, width = 10, height = 10) |
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} |
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} |
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}) |
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observeEvent(input$popexport,{ |
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if (input$phenotype == "Pop"){ |
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route<-cito_dir |
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ws<-open_flowjo_xml(paste0(route,"Populations.wsp")) |
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gs<-flowjo_to_gatingset(ws, name="All Samples") |
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sampleNames(gs)<-sapply(sampleNames(gs), function(x) strsplit(x, "Pop ")[[1]][2]) %>% |
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gsub("[[:space:]][0-9]*.fcs_.[0-9]*","", . , perl = T) |
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nodes<-sapply(strsplit(gs_get_pop_paths(gs), "/"), tail, 1) |
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nodes<-nodes[grepl("_",nodes)] |
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pop<-gs_pop_get_stats(gs, nodes=nodes,type="percent") %>% as.data.frame %>% mutate(percent=percent*100) |
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pop[,"pop"]<-gsub("_","",pop$pop) |
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pop$pop<-gsub(" ","_",pop$pop) |
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pop$pop<-gsub("+","pos",pop$pop, fixed=T) |
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pop$pop<-gsub("-","neg",pop$pop, fixed=T) |
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pop<-rename(pop, "samples"="sample") |
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pop$percent<-round(pop$percent, digits=2) |
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pop_sp<-pop %>% spread(pop, percent) |
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pop_sql<-sqlFetch(dta, "POPULATIONS") %>% slice(0) |
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pop_sp<-pop_sp %>% merge(pop_sql, all=T) %>% select(colnames(pop_sql)) |
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vartypes<-rep("Number", pop_sp %>% select(-samples) %>% colnames %>% length) |
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names(vartypes)<-pop_sp %>% select(-samples) %>% colnames |
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sqlSave(dta, pop_sp, tablename="POPULATIONS", append = T, varTypes = vartypes, rownames = F) |
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print("Tabla POPULATIONS sincronizada.") |
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} |
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if (input$phenotype == "IC"){ |
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route<-cito_dir |
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ws<-open_flowjo_xml(paste0(route,"IC.wsp")) |
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gs<-flowjo_to_gatingset(ws, name="All Samples") |
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sampleNames(gs)<-sapply(sampleNames(gs), function(x) strsplit(x, "ICs ")[[1]][2]) %>% |
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gsub("[[:space:]][0-9]*.fcs_.[0-9]*","", . , perl = T) |
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nodes<-gs_get_pop_paths(gs) |
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# nodes<-gsub("â\u0081»", "-", nodes) |
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# nodes<-gsub("â\u0081º", "+", nodes) |
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nodes<-nodes[grepl("CTLA4", nodes)] |
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nodes<-nodes[!grepl("CD4$|CD8$|CTLA4$|TIM3$|PD1$|LAG3$|TIGIT$|/CTLA4â\u0081»$|/TIM3â\u0081»$|/PD1â\u0081»$|/LAG3â\u0081»$|/TIGITâ\u0081»$", nodes)] |
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pop<-gs_pop_get_stats(gs, nodes=nodes,type="percent") %>% as.data.frame %>% mutate(percent=percent*100) |
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pop$percent<-round(pop$percent, digits=2) |
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pop$pop<-gsub("â\u0081»", "n", pop$pop) |
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pop$pop<-gsub("â\u0081º", "p", pop$pop) |
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pop$pop<-gsub(" ", "_", pop$pop) |
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pop["Type"]<-"ab" |
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pop[grepl("iso|ISO|Iso",pop$sample),"Type"]<-"iso" |
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pop$sample<-gsub("iso|ISO|Iso|ab|AB|Ab| ","",pop$sample) |
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pop_sp<-pop %>% spread(Type, percent) |
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pop_sp["Net"]<-pop_sp$ab |
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pop_sp[!grepl("CTLA4n_LAG3n_PD1n_TIGITn_TIM3n",pop_sp$pop),"Net"]<-pop_sp[!grepl("CTLA4n_LAG3n_PD1n_TIGITn_TIM3n",pop_sp$pop),"ab"]-pop_sp[!grepl("CTLA4n_LAG3n_PD1n_TIGITn_TIM3n",pop_sp$pop),"iso"] |
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pop_sp$Net[pop_sp$Net < 0]<-0 |
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pop_sp["Population"]<-str_extract(pop_sp$pop, "/CD[4,8]{1}/") %>% gsub("/","",.) |
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pop_sp$pop<-sapply(strsplit(pop_sp$pop, "/"), tail, 1) |
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pop_sp<-pop_sp %>% select(-ab,-iso) %>% spread(pop,Net) |
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pop_sp$`CTLA4n_LAG3n_PD1n_TIGITn_TIM3n`<- pop_sp %>% select(-`CTLA4n_LAG3n_PD1n_TIGITn_TIM3n`) %>% group_by(sample,Population) %>% |
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gather(pop, value, -sample,-Population) %>% summarise(n=100-sum(value)) %>% pull(n) |
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pop_sp <- rename(pop_sp, "samples"="sample") |
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vartypes<-rep("Number", pop_sp %>% select(-samples, -Population) %>% colnames %>% length) |
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names(vartypes)<-pop_sp %>% select(-samples, -Population) %>% colnames |
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sqlSave(dta, pop_sp, tablename="IC", append = T, varTypes = vartypes, rownames = F) |
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print("Tabla IC sincronizada.") |
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} |
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}) |
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## scRNAseq ---- |
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output$PATID = renderUI({ |
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output$PATID = renderUI({ |
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observeEvent(input$goButton, {}) |
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observeEvent(input$goButton, {}) |
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sc_cod<-sqlFetch(dta, "CNAG") %>% pull(CODIGO) |
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sc_cod<-sqlFetch(dta, "CNAG") %>% pull(CODIGO) |
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