Two Reactives Error Invalid Argument to Unary Operator - r

Question

I am trying to build an app that displays a .csv file in table format. The user can choose with radio buttons one of two ways to display the table. I have defined those two ways with the filedata() and data_ranked_words() reactives.
To reproduce this error, please first run this code chunk to get a small subset of my data:
test = rbind(
c(0.00000009, 0.00000009, 0.00046605, 0.00015541, 0.00215630),
c(0.00000016, 0.00137076, 0.00000016, 0.00000016, 0.00000016),
c(0.00012633, 0.00000014, 0.00000014, 0.00000014, 0.00075729),
c(0.00000013, 0.00000013, 0.00000013, 0.00000013, 0.00062728)
)
colnames(test) = c('church', 'appearance', 'restrain', 'parity', 'favor')
rownames(test) = NULL
test = as.data.frame(test)
write.csv(test, 'test.csv', row.names = FALSE)
You will see that you get an Error invalid argument to binary operator as soon as the program launches. Then choose test.csv off your filesystem in your working directory and you will see that the error persists while 'Word View' is selected, but the table correctly displays while 'Probability View' is selected.
This app is very simple. The problem occurs in line 66 temp = matrix(row.names(data)[apply(-data, 2, order)], nrow(data)). It doesn't like the -data within the apply. However, try as I might, I have not been able to reproduce this error just working in the R console, outside of shiny. In regular R, this line runs just fine.
What I am trying to do is display two different tables when the user selects the radio buttons. 'Probability View' is the raw table as is, and 'Word View' is the table with some operations on it (lines 61-71). I can't figure this one out!
Here is my app:
library(shiny)
library(markdown)
library(DT)
library(D3TableFilter)
options(shiny.maxRequestSize=50*1024^2)
# ui.R
#-------------------------------------------------------------------------------------
ui <- shinyUI(
navbarPage("Topic Model App v1.0",
tabPanel("From CSV",
sidebarLayout(
sidebarPanel(
# Define what's in the sidebar
fileInput("file",
"Choose CSV files from directory",
multiple = TRUE,
accept=c('text/csv',
'text/comma-separated-values,text/plain',
'.csv')),
radioButtons('toggle', 'Choose one:',
list('Word View', 'Probability View'))
),
# Define what's in the main panel
mainPanel(
title = 'Topic Model Viewer',
# How wide the main table will be
fluidRow(
column(width = 12, d3tfOutput('data'))
)
)
)
)
)
)
# server.R
#-------------------------------------------------------------------------------------
server <- shinyServer(function(input, output, session) {
# Set up the dataframe for display in the table
# Define 'filedata()' as the .csv file that is uploaded
filedata <- reactive({
infile <- input$file
if (is.null(infile)) {
# User has not uploaded a file yet
return(NULL)
}
# Read in .csv file and clean up
data = read.csv(infile$datapath)
data = t(data)
data = as.data.frame(data)
colnames(data) = paste0(rep('topic', ncol(data)), 1:ncol(data))
data = format(data, scientific = FALSE)
data
})
#PROBLEM
# The ranked and ordered csv file
data_ranked_words <- reactive({
# Sort each column by probability, and substitute the correct word into that column
# This will essentially rank each word for each topic
# This is done by indexing the row names by the order of each column
data = filedata()
temp = matrix(row.names(data)[apply(-data, 2, order)], nrow(data))
temp = as.data.frame(temp)
colnames(temp) = paste0(rep('topic', ncol(data)), 1:ncol(data))
temp
})
# Create table
output$data <- renderD3tf({
tableProps <- list(
rows_counter = TRUE,
rows_counter_text = "Rows: ",
alternate_rows = TRUE
);
# Radio buttons
# The reason why the extensions are in this if() is so that sorting can be
# activated on Probability View, but not Word View
if(input$toggle=='Word View'){
df = data_ranked_words()
extensions <- list(
list( name = "colsVisibility",
text = 'Hide columns: ',
enable_tick_all = TRUE
),
list( name = "filtersVisibility",
visible_at_start = FALSE)
)
} else if(input$toggle=='Probability View'){
df = filedata()
extensions <- list(
list(name = "sort"), #this enables/disables sorting
list( name = "colsVisibility",
text = 'Hide columns: ',
enable_tick_all = TRUE
),
list( name = "filtersVisibility",
visible_at_start = FALSE)
)
}
if(is.null(filedata())){
} else{
d3tf(df,
tableProps = tableProps,
extensions = extensions,
showRowNames = TRUE,
tableStyle = "table table-bordered")
}
})
# This line will end the R session when the Shiny app is closed
session$onSessionEnded(stopApp)
})
# Run app in browser
runApp(list(ui=ui,server=server), launch.browser = TRUE)

Answer 1

So a couple of problems are interacting here to make things difficult to diagnose:
It is running through and trying to execute before the data is defined. The "modern" way to avoid that is to use a req(input$file) - which is now inserted in the filedata reactive. Note that will break the entire chain from executing until input$file is defined in the shiny ui.
The data = format(data, scientific = FALSE) is converting your columns to vectors of type "AsIs", which the unitary minus command does not know how to operate on. It is commented out of filedata() now.
To get that functionality of suppressing the scientific notation back, the was moved to right after where df is created by filedata() before it is displayed in d3tf.
Note: I found it interesting that options with scipen did not work here. Not sure why that is the case, but this AsIs class does the trick.
Here is the adjusted code:
library(shiny)
library(markdown)
library(DT)
library(D3TableFilter)
options(shiny.maxRequestSize=50*1024^2)
# ui.R
#-------------------------------------------------------------------------------------
ui <- shinyUI(
navbarPage("Topic Model App v1.0",
tabPanel("From CSV",
sidebarLayout(
sidebarPanel(
# Define what's in the sidebar
fileInput("file",
"Choose CSV files from directory",
multiple = TRUE,
accept=c('text/csv',
'text/comma-separated-values,text/plain',
'.csv')),
radioButtons('toggle', 'Choose one:',
list('Word View', 'Probability View'))
),
# Define what's in the main panel
mainPanel(
title = 'Topic Model Viewer',
# How wide the main table will be
fluidRow(
column(width = 12, d3tfOutput('data'))
)
)
)
)
)
)
# server.R
#-------------------------------------------------------------------------------------
server <- shinyServer(function(input, output, session) {
# Set up the dataframe for display in the table
# Define 'filedata()' as the .csv file that is uploaded
filedata <- reactive({
req(input$file)
infile <- input$file
if (is.null(infile)) {
# User has not uploaded a file yet
return(NULL)
}
# Read in .csv file and clean up
data = read.csv(infile$datapath)
data = t(data)
data = as.data.frame(data)
colnames(data) = paste0(rep('topic', ncol(data)), 1:ncol(data))
# data = format(data, scientific = FALSE)
data
})
#PROBLEM
# The ranked and ordered csv file
data_ranked_words <- reactive({
# Sort each column by probability, and substitute the correct word into that column
# This will essentially rank each word for each topic
# This is done by indexing the row names by the order of each column
data = filedata()
temp = matrix(row.names(data)[apply(-data, 2, order)], nrow(data))
temp = as.data.frame(temp)
colnames(temp) = paste0(rep('topic', ncol(data)), 1:ncol(data))
temp
})
# Create table
output$data <- renderD3tf({
tableProps <- list(
rows_counter = TRUE,
rows_counter_text = "Rows: ",
alternate_rows = TRUE
);
# Radio buttons
# The reason why the extensions are in this if() is so that sorting can be
# activated on Probability View, but not Word View
if(input$toggle=='Word View'){
df = data_ranked_words()
extensions <- list(
list( name = "colsVisibility",
text = 'Hide columns: ',
enable_tick_all = TRUE
),
list( name = "filtersVisibility",
visible_at_start = FALSE)
)
} else if(input$toggle=='Probability View'){
df = filedata()
df = format(df, scientific = FALSE)
extensions <- list(
list(name = "sort"), #this enables/disables sorting
list( name = "colsVisibility",
text = 'Hide columns: ',
enable_tick_all = TRUE
),
list( name = "filtersVisibility",
visible_at_start = FALSE)
)
}
if(is.null(filedata())){
} else{
d3tf(df,
tableProps = tableProps,
extensions = extensions,
showRowNames = TRUE,
tableStyle = "table table-bordered")
}
})
# This line will end the R session when the Shiny app is closed
session$onSessionEnded(stopApp)
})
# Run app in browser
runApp(list(ui=ui,server=server), launch.browser = TRUE)
And here is a screen shot of it running: