How to plot heatmap with R shiny - r

Question

I am working with R shiny for pheatmap, I want to read files and draw heatmaps, but it did not work. The csv file could be read, however, the content could not be seen from the web, and the heatmap could not be drawn.
library(shiny)
library(pheatmap)
ui = fluidPage("Test",
sidebarPanel(
fileInput("file1", "Choose CSV File",
accept = c(
"text/csv",
"text/comma-separated-values,text/plain",
".csv")
),
tags$hr(),
checkboxInput("header", "Header", TRUE)
),
tabPanel('map',
sidebarLayout(
sidebarPanel('side',
actionButton('getHmap', 'get heatmap')
),
mainPanel('main',
plotOutput("themap")
)
))
)
server = function(input, output, session) {
a <- reactive({
inFile <- input$file1
if (is.null(inFile))
return(NULL)
tbl <- read.csv(inFile$datapath, header=input$header, sep=input$sep, dec = input$dec)
return(tbl)
})
output$table.output <- renderTable({
a()
})
observeEvent(input$getHmap, {
row.names(a) <- a$Name
a <- a[,-1]
a[is.na(a)] <- 0
output$themap = renderPlot({
pheatmap(a)
})
})
}
shinyApp(ui, server)
```[![The original data I used][1]][1]
[1]: https://i.stack.imgur.com/S83cH.png

Answer 1

This could be a full working example. This seems to work at my end. The following changes were made:
Added tableOutput("table.output") to ui
Simplified read.csv as inputs for sep and dec were missing
Created plotData function as eventReactive to plot heatmap with action button
Converted data to matrix before adding rownames for plot
The output$themap calls the plotData function
library(shiny)
library(pheatmap)
ui = fluidPage("Test",
sidebarPanel(
fileInput("file1", "Choose CSV File",
accept = c(
"text/csv",
"text/comma-separated-values,text/plain",
".csv")
),
tags$hr(),
checkboxInput("header", "Header", TRUE)
),
tabPanel('map',
sidebarLayout(
sidebarPanel('side',
actionButton('getHmap', 'get heatmap')
),
mainPanel('main',
plotOutput("themap"),
tableOutput("table.output")
)
))
)
server = function(input, output, session) {
a <- reactive({
inFile <- input$file1
if (is.null(inFile))
return(NULL)
tbl <- read.csv(inFile$datapath, header=input$header) #, sep=input$sep, dec = input$dec)
return(tbl)
})
output$table.output <- renderTable({
a()
})
plotdata <- eventReactive(input$getHmap, {
a <- as.matrix(a()[-1])
row.names(a) <- a()$Name
a[is.na(a)] <- 0
a
})
output$themap = renderPlot({
pheatmap(plotdata())
})
}
shinyApp(ui, server)