Using Shiny, query and display data - r

Question

Issues I am having couple of issues with (a) Display the data in interactive mode using Rshiny (2) Querying the results from mongodb Query. My codes are given below, it seems to work as independent pieces but doesnt coalesce well.
For Problem (a), I have previously used Output$values and that seems to work. Commented out in the code
For Problem (b), I have used mongolite R package to query the data and used reactive for passing the query.
library(data.table)
library(tidyverse)
library(shiny)
library(mongolite)
epi <- read.csv("./data/Genes.csv", header=T)
label = "gene"
epilist <- data.frame(epi$gene, label)
names(epilist) = c("value", "label")
df <- read.table("./data/CCLE_meta.csv", header=TRUE, sep=",", na.strings="NA", fill=TRUE)
dd <- data.frame((df$Tissue))
names(dd) = "Tissue"
cell1= dd %>% add_row(Tissue = "all")
label = "Tissue"
cell <- data.frame(cell1$Tissue, label)
names(cell) = c("value", "label")
ui <- fluidPage(
titlePanel("Dependencies for EpiGenes"),
sidebarLayout(
sidebarPanel(
selectizeInput("epiInput","gene", choices=NULL, selected=NULL),
selectizeInput("cellInput","Tissue", choices=NULL, selected=NULL),
textOutput("values")
),
mainPanel(
tabsetPanel(type = "tabs",
tabPanel("Fusions", tableOutput("table")),
tabPanel("CancerGD", tableOutput("table")),
tabPanel("CCLEmeta", tableOutput("table")),
tabPanel("EpiGenes", tableOutput("table"))
)
)
)
)
server <- function(input, output, session) {
updateSelectizeInput(session, 'epiInput',
choices = epilist$value,
server = TRUE)
updateSelectizeInput(session, 'cellInput',
choices = cell$value,
server = TRUE)
#output$values <- renderText({
# paste(input$epiInput, input$cellInput)
#})
### Looking into Epi Genes
con1 <- mongo(collection = "Genes", db = "discovery", url = "mongodb://127.0.0.1:27017")
data.for.table1 <- reactive({
query.foo <- paste0('{"gene" : epiInput}')
con1$find(query = query.foo, limit = 100)
})
output$EpiGenes <- renderDataTable({
data.for.table1()
})
### Looking into Cell Line Metadata
con0 <- mongo(collection = "CellLine", db = "discovery", url = "mongodb://127.0.0.1:27017")
data.for.table0 <- reactive({
query.foo <- paste0('{"Tissue" : input$cellInput}')
con0$find(query = query.foo, limit = 100)
})
output$CCLEmeta <- renderDataTable({
data.for.table0()
})
### Looking into fusion genes
con2 <- mongo(collection = "fusions", db = "discovery", url = "mongodb://127.0.0.1:27017")
data.for.table2 <- reactive({
query.foo <- paste0('{"gene" : input$epiInput}')
con2$find(query = query.foo, limit = 100)
})
output$Fusions <- renderDataTable({
data.for.table2()
})
### Looking into CancerGD
con3 <- mongo(collection = "CancerGD", db = "discovery", url = "mongodb://127.0.0.1:27017")
data.for.table3 <- reactive({
query.foo <- paste0('{"gene" : input$epiInput}')
con3$find(query = query.foo, limit = 100)
})
output$CancerGD <- renderDataTable({
data.for.table3()
})
# Automatically disconnect when connection is removed
rm(con0)
rm(con1)
rm(con2)
rm(con3)
gc()
}
shinyApp(ui, server)
The first expected output is an app to allow users to query from the list of genes and tissue. The second expected output is display query results in its appropriate tab (From 4 collections from database discovery). The current result is an app with no ability to query.

Answer 1

I was able to make some changes to the code and the error/hanging I now get is
"Imported 0 records. Simplifying into dataframe..."
Any insight into the error will be helpful.
The improvements to the codes are as follows;
(a) SidebarPanel
selectizeInput("epiInput","gene", choices=gg),
selectizeInput("cellInput","Tissue", choices=cc),
(b) Connecting to MongoDB
con2 <- mongo(collection="fusions", db="discovery", url="mongodb://localhost:27017", verbose = TRUE)
fusResults <- reactive({
region <- list(gene = input$epiInput)
query.foo <- paste0('{ "gene" : "',region , '"}')
fs <- con2$find(query = query.foo, limit = 100)
return(fs)
})
output$fus_results <- renderDataTable({
fusResults()
})