How to solve the error in highcharOutput in shiny tool? - r

Question

I'm working on cancer data from TCGA.
Im new to shiny and creating web applications (learning it!!)
I'm working on a shiny tool to plot the volcanoplot using highcharter package.
sometimes I'm successfully able to plot the volcanoplot in the UI. but sometimes it fails to plot it and throws an error saying,
"An error has occurred!
could not find function "highchartOutput"
and one warning message is given for the error;
Listening on http://127.0.0.1:5335
Warning: Error in highchartOutput: could not find function "highchartOutput"
83: dots_list
82: div
81: tabPanel
I think there is some problem with the tabset panel.
is this error has anything to do with indentation? (wherever I adjust the brackets it works magically. not sure how it works for sometimes.)
I am attaching the UI and server files with this post.
code is attached for one type of comparison
UI file below:
library(shiny)
# Define UI for application
shinyUI(fluidPage(
# Application title
titlePanel("miR-Gyn-Explorer"),
# Sidebar with a slider input for number of bins
sidebarLayout(
sidebarPanel(
## select the count matrix
selectInput("file", label = h3("Count Matrix"),
choices = list("Stage I - Normal" = list("TCGA-BRCA" = "Data/TCGA-BRCASI_NT.rda", "TCGA-UCEC" = "Data/TCGA-UCECSI_NT.rda"))),
## select the phenodata of samples
selectInput("phenofile", label = h3("Sample Phenodata"),
choices = list("Stage I - Normal" = list("TCGA-BRCA" = "Data/TCGA-BRCA_phenoSI_NT.rda", "TCGA-UCEC" = "Data/TCGA-UCEC_phenoSI_NT.rda"))),
submitButton("Update View")
),
# Show a plot of the generated distribution
mainPanel(
tabsetPanel(
tabPanel("DEmiRNA", DT::dataTableOutput("DEmiRNA"),
"Volcano-Plot", highchartOutput("volcanoPlot", height = "500px"))
#tabPanel("miRNA-Targets", DT::dataTableOutput('miRTarget'),
#plotOutput("GO"))
)
)
)
)
)
server file:
library(shiny)
library(R.utils)
##function to find the DEmiRNA by edgeR method
library(limma)
library(edgeR)
library(DT)
library(dplyr)
library(multiMiR)
library(miRBaseConverter)
library(ggplot2)
#library(ggrepel)
library(tidyverse)
library(highcharter)
library(org.Hs.eg.db)
library(clusterProfiler)
library(purrr)
gdcDEmiRNA <- function(counts, groups, comparison, filter=TRUE) {
## method = edgeR
dge = DGEList(counts = counts, samples = groups)
group <- factor(groups$group)
design <- model.matrix(~0+group)
colnames(design) <- levels(group)
contrast.matrix <- makeContrasts(contrasts=comparison,
levels=design)
keep = filterByExpr(dge,design)
dge <- dge[keep,,keep.lib.sizes = TRUE]
dge <- calcNormFactors(dge)
dge <- estimateDisp(dge, design)
fit <- glmFit(dge, design)
lrt <- glmLRT(fit, contrast=contrast.matrix)
DEGAll <- lrt$table
DEGAll$FDR <- p.adjust(DEGAll$PValue, method = 'fdr')
o <- order(DEGAll$FDR)
DEGAll <- DEGAll[o,]
return (DEGAll)
}
# Define server logic required to perform the DEmiRNA analysis
server <- function(input, output) {
d <- reactive({
#DEmiRNA calculation
file <- load(input$file)
phenofile <- load(input$phenofile)
if(file == "SI_NT"){
if(phenofile == "phenoSI_NT"){
DEmiRNA <- gdcDEmiRNA(counts = SI_NT, groups = phenoSI_NT,
comparison = 'StageI-Normal')
}
}
})
output$DEmiRNA <- DT::renderDataTable({
mir <- d()
#mir <- mir[mir$FDR < input$FDR,]
})
output$volcanoPlot <- renderHighchart({
x <- d()
x$mirna <- rownames(x)
x$sig <- ifelse(x$PValue < 0.05 & abs(x$logFC) > 0.57, "DEmiRNA", "Not Regulated")
hc <- highchart() %>%
hc_add_series(x, "scatter", hcaes(logFC, -log10(PValue), group = sig, value = mirna),
color = c('rgba(67, 67, 72, 0.6)', 'rgba(124, 181, 236, 0.6)'),
enableMouseTracking = c(TRUE, TRUE),
showInLegend = TRUE, marker = list(radius = 4)) %>%
hc_tooltip(pointFormat = "{point.value}", headerFormat = "") %>%
hc_xAxis(title = list(text = "Log fold change"), gridLineWidth = 1,
tickLength = 0, startOnTick = "true", endOnTick = "true", min = -6, max = 6) %>%
hc_yAxis(title = list(text = "-Log10(p-value)")) %>%
hc_chart(zoomType = "xy", width=700) %>%
hc_exporting(enabled = TRUE, filename = "volcano")
hc
})
}
any comment and help from you guys is appreciated
Thank you in advance!
-Ankita