Added code from local repo on my personal github

R-Shiny-App-Practice-master/.gitignore

@@ -0,0 +1,39 @@
+# History files
+.Rhistory
+.Rapp.history
+
+# Session Data files
+.RData
+
+# User-specific files
+.Ruserdata
+
+# Example code in package build process
+*-Ex.R
+
+# Output files from R CMD build
+/*.tar.gz
+
+# Output files from R CMD check
+/*.Rcheck/
+
+# RStudio files
+.Rproj.user/
+
+# produced vignettes
+vignettes/*.html
+vignettes/*.pdf
+
+# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
+.httr-oauth
+
+# knitr and R markdown default cache directories
+*_cache/
+/cache/
+
+# Temporary files created by R markdown
+*.utf8.md
+*.knit.md
+
+# R Environment Variables
+.Renviron

README.md

@@ -1,2 +1,2 @@
-# clustifyr-web-app
-An R Shiny App to help with scRNA-seq benchmarking and analysis with Clustifyr
+# R-Shiny-App-Practice
+A repository to prepare myself for writing an R shiny app for the scRNA-seq atlas web tool

rsconnect/shinyapps.io/sidhantpuntambekar/scRNA-seq-atlas.dcf

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+name: scRNA-seq-atlas
+title: scRNA-seq-atlas
+username:
+account: sidhantpuntambekar
+server: shinyapps.io
+hostUrl: https://api.shinyapps.io/v1
+appId: 2890325
+bundleId: 3671701
+url: https://sidhantpuntambekar.shinyapps.io/scRNA-seq-atlas/
+when: 1601067752.08105
+asMultiple: FALSE
+asStatic: FALSE

scRNA-seq-atlas/app.R

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+library(shiny)
+library(dplyr)
+library(readr)
+library(tools)
+library(clustifyr)
+library(rsconnect)
+options(shiny.maxRequestSize = 1500*1024^2)
+options(repos = BiocManager::repositories())
+options(shiny.reactlog = TRUE)
+
+# Define UI for data upload app ----
+ui <- fluidPage(
+
+    # App title ----
+    titlePanel("Clustifyr Reference Matrix Generation"),
+
+    # Sidebar layout with input and output definitions ----
+    sidebarLayout(
+
+        # Sidebar panel for inputs ----
+        sidebarPanel(
+
+            # Input: Select a file ----
+            fileInput("file1", "Choose Matrix File",
+                      multiple = TRUE,
+                      accept = c("text/csv",
+                                 "text/comma-separated-values,text/plain",
+                                 ".csv",
+                                 '.xlsx',
+                                 ".tsv",
+                                 ".rds",
+                                 ".rda"),
+            ),
+            fileInput("file2", "Choose Metadata File",
+                      multiple = FALSE,
+                      accept = c("text/csv",
+                                 "text/comma-separated-values,text/plain",
+                                 ".csv",
+                                 '.xlsx',
+                                 ".tsv",
+                                 ".rds",
+                                 ".rda"),
+                      ),
+
+            tags$hr(),
+
+            # Input: Checkbox if file has header ----
+            checkboxInput("header", "Header", TRUE),
+
+
+            # Horizontal line ----
+            tags$hr(),
+
+            # Input: Select separator ----
+            radioButtons("sep", "Separator",
+                         choices = c(Tab = "\t"),
+                         selected = ","),
+
+            # Input: Select number of rows to display ----
+            radioButtons("disp", "Display",
+                         choices = c(Head = "head",
+                                     All = "all"),
+                         selected = "head")
+
+        ),
+
+        # Main panel for displaying outputs ----
+        mainPanel(
+
+            # Output: Data file ----
+            tableOutput("contents")
+
+        )
+
+    )
+)
+
+# Define server logic to read selected file ----
+server <- function(input, output) {
+
+    output$contents <- renderTable({
+
+        # input$file1 will be NULL initially. After the user selects
+        # and uploads a file, head of that data file by default,
+        # or all rows if selected, will be shown.
+        file <- input$file1
+        fileTypeFile1 <- tools::file_ext(file$datapath)
+        req(file)
+        # when reading semicolon separated files,
+        # having a comma separator causes `read.csv` to error
+            if (fileTypeFile1 == "csv")
+            {
+                df1 <- read.csv(file$datapath,
+                                header = input$header,
+                                sep = input$sep,
+                                quote = input$quote)
+            }
+            else if (fileTypeFile1 == "tsv")
+            {
+                df1 <- read_tsv(file$datapath,
+                                header = input$header,
+                                quote = input$quote)
+            }
+            else
+            {
+                df1 <- load(file$datapath)
+            }
+
+            #file 1
+            if(input$disp == "head") {
+                return(head(df1))
+            }
+            else {
+                return(df1)
+            }
+        }
+    )
+
+    output$file2Contents <- renderTable({
+        file <- input$file2    
+        fileTypeFile2 <- tools::file_ext(file$datapath)
+        req(file)
+        if (fileTypeFile2 == "csv")
+        {
+            df2 <- read.csv(file$datapath,
+                            header = input$header,
+                            sep = input$sep,
+                            quote = input$quote)
+        }
+        else if (fileTypeFile2 == "tsv")
+        {
+            df2 <- read_tsv(file$datapath,
+                            header = input$header,
+                            quote = input$quote)   
+        }
+        else
+        {
+            df2 <- load(file$datapath)
+        }
+
+        #file 2
+        if(input$disp == "head") {
+            return(head(df2))
+        }
+        else {
+            return(df2)
+        }
+    }
+)
+
+    output$reference <- renderTable({
+        req(input$file1)
+        req(input$file2)
+        fileTypeFile1 <- file_ext(input$file1)
+        fileTypeFile2 <- file_ext(input$file2)
+        df1 <- read.csv(input$file1$datapath,
+                        header = input$header,
+                        sep = input$sep,
+                        quote = input$quote)
+        df2 <- read.csv(input$file2$datapath,
+                        header = input$header,
+                        sep = input$sep,
+                        quote = input$quote)
+        reference_matrix <- average_clusters(mat = df1, metadata = df2$cellCol, if_log = TRUE)
+        head(reference_matrix)
+    })
+
+}
+
+# Create Shiny app ----
+shinyApp(ui, server)