Plot data after browsing input files with Shiny - r

Question

I am trying to build a Shiny App that does the following:
1) Browse a value file that looks like
Sample x y
A 1 3
B 2 1
C 3 6
D 4 4
2) Browse a second info file,
Sample Country Status
A US OK
B UK OK
C UK NOPE
D US OK
3) When I press a Submit button,
4) I merge the two files by the Sample column,
5) And make a scatter plot with ggplot, with a dropdown menu that allows me to color the points according to the names of the columns from the info file.
With the code below, I am facing two problems: (i) after I load my files and press the Submit button, nothing happens, and (ii) how could I mention in my selectInput block for my dropdown menu the number of possible choices (assuming I do not know them in advance)?
library(shiny)
library(ggplot2)
ui <- fluidPage(
sidebarLayout(
sidebarPanel(
fileInput(
inputId = "user_value_file",
label = "Choose a file with numeric values"
),
fileInput(
inputId = "user_info_file",
label = "Choose a file with sample info"
),
actionButton(
inputId = "my_button",
label = "Submit"
)
),
mainPanel(
# browse sample annotation file
selectInput(
inputId = "info_col",
label = "Choose an info to color",
choices = c("Country", "Status") # I am cheating here because I know in advance what are the colnames of the info file
),
# outputs
plotOutput(
outputId = "my_scatter_plot"
)
)
)
)
server <- function(input, output) {
output$contents <- renderTable(
{
valueFile <- input$user_value_file
if (is.null(valueFile))
return(NULL)
infoFile <- input$user_info_file
if (is.null(infoFile))
return(NULL)
}
)
randomVals <- eventReactive(
input$goButton,
{
my_val <- read.table(valueFile$datapath, header = T, sep = "\t")
my_info <- read.table(infoFile$datapath, header = T, sep = "\t")
df <- merge(my_val, my_info, by="Sample")
output$my_scatter_plot <- renderPlot(
{
ggplot(df, aes_string(x=df$x, y=df$y, color=input$info_col)) +
geom_point()
}
)
}
)
}
shinyApp(ui = ui, server = server)

Answer 1

A few things noted to get it working:
the inputID in the layout needs to match the server renderTable parameters (e.g., input$goButton should be input$my_button)
renderPlot was moved from eventReactive, and calls randomVals to get the data frame df
To get choices from the user info file, added session to server function and updateSelectInput (note depending on that file structure you probably want to do something like remove first column name or other changes)
Otherwise left things as they are. Please let me know if this has the behavior you were looking for.
library(shiny)
library(ggplot2)
ui <- fluidPage(
sidebarLayout(
sidebarPanel(
fileInput(
inputId = "user_value_file",
label = "Choose a file with numeric values"
),
fileInput(
inputId = "user_info_file",
label = "Choose a file with sample info"
),
actionButton(
inputId = "my_button",
label = "Submit"
)
),
mainPanel(
# browse sample annotation file
selectInput(
inputId = "info_col",
label = "Choose an info to color",
choices = NULL # Get colnames from user_info_file later on
),
# outputs
plotOutput(
outputId = "my_scatter_plot"
)
)
)
)
server <- function(input, output, session) {
output$contents <- renderTable({
valueFile <- input$user_value_file
if (is.null(valueFile))
return(NULL)
infoFile <- input$user_info_file
if (is.null(infoFile))
return(NULL)
})
randomVals <- eventReactive(input$my_button, {
my_val <- read.table(input$user_value_file$datapath, header = T, sep = "\t")
my_info <- read.table(input$user_info_file$datapath, header = T, sep = "\t")
updateSelectInput(session, "info_col", "Choose an info to color", choices = names(my_info)[-1])
merge(my_val, my_info, by="Sample")
})
output$my_scatter_plot <- renderPlot({
df <- randomVals()
ggplot(df, aes_string(x=df$x, y=df$y, color=input$info_col)) +
geom_point()
})
}
shinyApp(ui, server)