library(shiny)
ui <- fluidPage(
titlePanel("Arabidopsis EcosGEx"),
sidebarLayout(
sidebarPanel(
textInput("agi", "Entre your AGI ID:"),
helpText("Example: AT5G61590"),
actionButton("find", "Find"),
helpText("It will take some time. Be patient after you hit Find."),
uiOutput("download")
),
mainPanel(
h3("Ecotype specific Gene Expression", align = "center"),
dataTableOutput("mytable"),
tabsetPanel(type = "tabs",
tabPanel("Plot", plotOutput("plot")),
tabPanel("Table", dataTableOutput("table")),
tabPanel("Summary", verbatimTextOutput("summary"))
)
)
)
)
###########################################################################
server <- function(input, output) {
#Load packages
library(data.table)
library(maptools)
library(maps)
library(ggmap)
library(ggplot2)
observeEvent(input$find, {
withProgress(message = 'Processing:', value = 0, {
incProgress(1/2, detail = paste("Finding your gene"))
#Read data.
expr <- read.csv("expr.csv", sep = "\t", row.names = 1)
cord <- read.csv("665_cord.csv")
#Taking the AGI ID and process the table.
agi_id <- toupper(input$agi)
gene <- t(expr[agi_id,])
gene_df <- as.data.frame(gene)
gene_expr <- setDT(gene_df, keep.rownames = TRUE)[]
colnames(gene_expr)[1] <- "gene_id"
all <- merge(x=gene_expr, y=cord, by= "gene_id", all=TRUE)
all_combined <- na.omit(all)
colnames(all_combined)[1] <- "Ecotype_ID"
incProgress(2/2, detail = paste("Printing table"))
#Printing the table to screen on table tab
output$table = renderDataTable({
all_combined
})
#Downlord the file
output$tabledownload <- downloadHandler(
filename = function() {
paste(toupper(input$agi), ".csv", sep = "")
},
content = function(file) {
write.csv(all_combined, file, row.names = FALSE)
}
)
#Downlord button (for table)
output$download <- renderUI({
if(!is.null(input$agi)) {
downloadButton("tabledownload", "Download Table")
}
})
})
})
}
shinyApp(ui = ui, server = server)
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