Improve Shiny with help text & pattern input (0dcec26a) · Commits · github_fork / ZUMIs

zUMIs-config_shiny.R

+101 −30

Original line number	Diff line number	Diff line
		@@ -9,62 +9,89 @@

		library(shiny)
		library(yaml)
		library(shinyBS)

		# Define UI for application
		ui <- fluidPage(
		# Application title
		theme = shinythemes::shinytheme("simplex"),
		titlePanel("zUMIs-config: Generate yaml file"),
		navlistPanel(id = "mainNav",widths = c(2, 10),
		tabPanel("Mandatory Parameters",
		#set basic things
		fluidRow(
		column(6,wellPanel(
		textInput(inputId="runID", label="Name of the run/project", placeholder="eg: my_zUMIs_run")
		textInput(inputId="runID", label="Name of the run/project:", placeholder="eg: my_zUMIs_run")
		)),
		shinyBS::bsTooltip(id="runID", title="This name will be used to label output files produced by zUMIs.",
		placement = "bottom", trigger = "hover",options = list(container = "body")),
		column(6,wellPanel(
		textInput(inputId="outDir", label="Full path to the output directory", placeholder="eg: /path/to/output")
		textInput(inputId="outDir", label="Path to the output directory:", placeholder="eg: /path/to/output"),
		shinyBS::bsTooltip(id="outDir", title="Please remember to give the full path, as relative paths may not work.",
		placement = "bottom", trigger = "hover",options = list(container = "body"))
		))
		),

		#STAR options


		# slider input for number of fastq reads
		fluidRow(
		h4("Input options:",style = "padding-left: 20px;"),
		column(4,wellPanel(
		sliderInput("nfiles", "Number of Input fastq files:", min = 1, max = 4,value = 2)
		sliderInput("nfiles", "Number of input fastq files:", min = 1, max = 4,value = 2),
		shinyBS::bsTooltip(id="nfiles", title="How many reads (including index reads) were obtained by your sequencing layout?",
		placement = "bottom", trigger = "hover",options = list(container = "body")),
		checkboxInput("patternsearch", "Search for sequence pattern in reads?", value = F),
		uiOutput("patternUI"), uiOutput("patternReadUI")
		)),
		column(8,wellPanel(
		uiOutput("fqUI")
		uiOutput("fqUI"),
		shinyBS::bsTooltip(id="fqUI", title="Please remember to give full paths, as relative paths may not work.",
		placement = "bottom", trigger = "hover",options = list(container = "body"))
		))
		),


		fluidRow(

		h4("In this section, fill only those fields that fit your input files:"),
		column(3,wellPanel(
		uiOutput("fqBCui")
		uiOutput("fqBCui"),
		shinyBS::bsTooltip(id="fqBCui", title="List any barcode (BC) ranges to be extracted from the reads. You can also extract several barcode ranges from the same read using comma-separation: 1-6,11-16 ",
		placement = "left", trigger = "hover",options = list(container = "body"))
		),offset = 1),
		column(3,wellPanel(
		uiOutput("fqUMIui")
		uiOutput("fqUMIui"),
		shinyBS::bsTooltip(id="fqUMIui", title="List any unique molecular identifier (UMI) ranges to be extracted from the reads.",
		placement = "bottom", trigger = "hover",options = list(container = "body"))
		)),
		column(3,wellPanel(
		uiOutput("fqCDNAui")
		uiOutput("fqCDNAui"),
		shinyBS::bsTooltip(id="fqCDNAui", title="List the cDNA range(s) in the reads to be mapped to the genome. May be one range (single-end) or two ranges (paired-end)",
		placement = "right", trigger = "hover",options = list(container = "body"))
		))
		),

		fluidRow(
		h4("Mapping/Reference options:",style = "padding-left: 20px;"),
		column(6,wellPanel(
		textInput(inputId="STARpath", label="Full path to the STAR index directory", placeholder="eg: /path/to/output"),
		textInput(inputId="GTFpath", label="Full path to the annotation GTF file", placeholder="eg: /path/to/output"),
		textInput(inputId="STARparams", label="Optional: Additional mapping parameters for STAR", value=""),
		numericInput(inputId = "NUMadditionalFA",label = "Optional: Number of additional reference sequences (eg. ERCC.fa)",value = 0,min = 0,step = 1)
		textInput(inputId="STARpath", label="Full path to the STAR index directory:", placeholder="eg: /path/to/output"),
		shinyBS::bsTooltip(id="STARpath", title="The STAR index should be generated without splice junction database. Please remember to give the full path, as relative paths may not work.",
		placement = "bottom", trigger = "hover",options = list(container = "body")),
		textInput(inputId="GTFpath", label="Full path to the annotation GTF file:", placeholder="eg: /path/to/output"),
		shinyBS::bsTooltip(id="GTFpath", title="Make sure the gene annotation matches the genome. Please remember to give the full path, as relative paths may not work.",
		placement = "bottom", trigger = "hover",options = list(container = "body")),
		textInput(inputId="STARparams", label="Optional: Additional mapping parameters for STAR:", value=""),
		shinyBS::bsTooltip(id="STARparams", title="You may list additional STAR mapping parameters. For instance, try trimming adapter sequenes using --clip3pAdapterSeq",
		placement = "top", trigger = "hover",options = list(container = "body")),
		numericInput(inputId = "NUMadditionalFA",label = "Optional: Number of additional reference sequences:",value = 0,min = 0,step = 1),
		shinyBS::bsTooltip(id="NUMadditionalFA", title="Here you can give additional reference sequences zUMIs should map to but are not integrated in the STAR index. For instance, you could add the ERCC spike-in reference on the fly (eg. ERCC.fa).",
		placement = "top", trigger = "hover",options = list(container = "body"))
		)),
		column(6,wellPanel(
		p(strong("Additional references:")),
		uiOutput("refUI")
		uiOutput("refUI"),
		shinyBS::bsTooltip(id="refUI", title="Please remember to give the full paths, as relative paths may not work.",
		placement = "top", trigger = "hover",options = list(container = "body"))
		))
		)

		@@ -75,9 +102,17 @@ ui <- fluidPage(
		column(6,wellPanel(
		h4("General options:"),
		numericInput("numThreads","Number of CPU Threads:",value=8,min=1,step=1),
		shinyBS::bsTooltip(id="numThreads", title="More CPU Threads increase processing speeds, but speed usually becomes I/O limited above 32 Threads.",
		placement = "bottom", trigger = "hover",options = list(container = "body")),
		numericInput("memLimit","Memory limit (Gb) 0 = no limit:",value=0,step=1),
		shinyBS::bsTooltip(id="memLimit", title="More memory usually speeds up processing. Note that this setting cannot prevent STAR from using as much RAM as necessary for the specified reference genome.",
		placement = "bottom", trigger = "hover",options = list(container = "body")),
		checkboxInput("makeStats",label="Produce summary statistics",value = T),
		selectInput("whichStage",label = "Start zUMIs from following stage:",choices = c("Filtering", "Mapping", "Counting", "Summarising"),selected = "Filtering",multiple = F)
		shinyBS::bsTooltip(id="makeStats", title="Plots and statistics files can be found in zUMIs_output/stats/.",
		placement = "bottom", trigger = "hover",options = list(container = "body")),
		selectInput("whichStage",label = "Start zUMIs from following stage:",choices = c("Filtering", "Mapping", "Counting", "Summarising"),selected = "Filtering",multiple = F),
		shinyBS::bsTooltip(id="whichStage", title="(Re)-Run the pipeline from the specified stage. Default: Filtering.",
		placement = "bottom", trigger = "hover",options = list(container = "body"))
		)),


		@@ -92,17 +127,27 @@ ui <- fluidPage(
		fluidRow(
		column(6,wellPanel(
		h4("Counting options:"),
		checkboxInput("countIntrons",label="Also count introns & exon+intron",value = T),
		textInput("downsamp",label = "Number of reads to downsample to. This value can be a fixed number of reads (e.g. 10000) or a desired range (e.g. 10000-20000). 0 invokes adaptive downsampling.",value = "0"),
		checkboxInput("countIntrons",label="Generate intron & exon+intron count tables?",value = T),
		shinyBS::bsTooltip(id="countIntrons", title="Exonic read count tables will by output in any case. Untick this box if you want to count exonic reads only.",
		placement = "top", trigger = "hover",options = list(container = "body")),
		textInput("downsamp",label = "Number of reads to downsample to:",value = "0"),
		shinyBS::bsTooltip(id="downsamp", title="This value can be a fixed number of reads (e.g. 10000) or a desired range (e.g. 10000-20000). You can also use several depths (e.g. 10000,20000,40000-50000). 0 invokes adaptive downsampling using median-absolute deviation of observed read counts.",
		placement = "bottom", trigger = "hover",options = list(container = "body")),
		selectInput("strand",label = "Is the library stranded?",choices = c("unstranded" = 0, "positively stranded" = 1, "negatively stranded" = 2),selected = "unstranded",multiple = F),
		numericInput("HamDist","Hamming distance collapsing of UMI sequences:",value=0,min=0,max=5,step=1),
		shinyBS::bsTooltip(id="HamDist", title="Note: Using this will considerably slow down the processing.",
		placement = "top", trigger = "hover",options = list(container = "body")),
		checkboxInput("doVelocity",label="Generate velocyto-compatible counting of intron-exon spanning reads. ATTENTION! This option is currently not implemented!",value = F),
		checkboxInput("countPrimary",label="Count the primary Hits of multimapping reads towards gene expression levels?",value = T),
		checkboxInput("twoPass",label="Perform basic STAR twoPass mapping?",value = T)
		shinyBS::bsTooltip(id="countPrimary", title="Untick this box if you want to count uniquely aligned reads only.",
		placement = "top", trigger = "hover",options = list(container = "body")),
		checkboxInput("twoPass",label="Perform STAR twoPass mapping?",value = T),
		shinyBS::bsTooltip(id="twoPass", title="Two-Pass mapping can improve the mapping by identifying novel splice-junctions.",
		placement = "top", trigger = "hover",options = list(container = "body"))
		)),
		column(6,wellPanel(
		h4("Barcode options:"),
		radioButtons(inputId = "barcodeChoice",label = "Type of barcode selection:",choices = c("Automatic","Number of top Barcodes","Barcod whitelist")),
		radioButtons(inputId = "barcodeChoice",label = "Type of barcode selection:",choices = c("Automatic","Number of top Barcodes","Barcode whitelist")),
		uiOutput("barcodeUI"),
		numericInput("HamBC","Hamming distance collapsing of close cell barcode sequences. ATTENTION! This option is currently not implemented!",value=0,min=0,max=5,step=1),
		numericInput("nReadsBC","Keep only the cell barcodes with atleast n number of reads",value=100,min=1,max=5,step=1)
		@@ -130,10 +175,22 @@ server <- function(input, output, session) {
		switch(input$barcodeChoice,
		"Automatic" = p(em("Intact barcodes will be detected automatically.")),
		"Number of top Barcodes" = numericInput(inputId = "BCnum",label = "Number of barcodes to consider:",value = 100, min = 10, step = 1),
		"Barcod whitelist" = textInput(inputId = "BCfile",label = "File to barcode whitelist to use:", value = "/fullpath/to/file.txt")
		"Barcode whitelist" = textInput(inputId = "BCfile",label = "File to barcode whitelist to use:", value = "/fullpath/to/file.txt")
		)
		})

		output$patternUI <- renderUI({
		if(input$patternsearch==T){
		textInput(inputId = "pattern", label = "Search for the following sequence:" , placeholder = "ACTGCTGC")
		}
		})

		output$patternReadUI <- renderUI({
		if(input$patternsearch==T){
		selectInput(inputId = "patternRead", label = "Search for the pattern in this read:" ,choices = paste("Read",1:input$nfiles),selected = "Read 1")
		}
		})

		output$refUI <- renderUI({
		if(input$NUMadditionalFA>0){
		lapply(1:input$NUMadditionalFA, function(i) {
		@@ -145,7 +202,7 @@ server <- function(input, output, session) {
		output$fqUI <- renderUI({
		if(input$nfiles>0){
		lapply(1:input$nfiles, function(i) {
		textInput(inputId = paste0("fqpath_",i),label = paste("Full path to fastq file",i),placeholder = "/path/to/read.fq.gz")
		textInput(inputId = paste0("fqpath_",i),label = paste("Full path to fastq file",i,":"),placeholder = "/path/to/read.fq.gz")
		})
		}
		})
		@@ -157,20 +214,20 @@ server <- function(input, output, session) {
		# })
		# }
		lapply(1:input$nfiles, function(i) {
		textInput(inputId = paste0("BC_",i),label = paste("Read",i,"BC"),placeholder = "eg: 1-6")
		textInput(inputId = paste0("BC_",i),label = paste("Read",i,"BC",":"),placeholder = "eg: 1-6")
		})

		})

		output$fqUMIui <- renderUI({
		lapply(1:input$nfiles, function(i) {
		textInput(inputId = paste0("UMI_",i),label = paste("Read",i,"UMI"),placeholder = "eg: 7-16")
		textInput(inputId = paste0("UMI_",i),label = paste("Read",i,"UMI",":"),placeholder = "eg: 7-16")
		})
		})

		output$fqCDNAui <- renderUI({
		lapply(1:input$nfiles, function(i) {
		textInput(inputId = paste0("cDNA_",i),label = paste("Read",i,"cDNA"),placeholder = "eg: 1-50")
		textInput(inputId = paste0("cDNA_",i),label = paste("Read",i,"cDNA",":"),placeholder = "eg: 1-50")
		})
		})

		@@ -211,11 +268,20 @@ server <- function(input, output, session) {
		names(bc_struc)<-c("cDNA","BC","UMI")
		bc_struc<-bc_struc[which( bc_struc != "" )]

		if(input$patternsearch==T & substr(input$patternRead,6,6)==i){
		seqf[[i]] <- list(
		"name" = input[[paste0("fqpath_",i)]],
		"base_definition" = paste0(names(bc_struc),"(",bc_struc,")"),
		"find_pattern" = input$pattern
		)
		}else{
		seqf[[i]] <- list(
		"name" = input[[paste0("fqpath_",i)]],
		"base_definition" = paste0(names(bc_struc),"(",bc_struc,")")
		)
		}

		}
		names(seqf) <- paste0("file",1:input$nfiles)

		#collect potential additional fasta files
		@@ -320,6 +386,11 @@ server <- function(input, output, session) {
		cdna_string <- substr(cdna_string,start = 6, stop = nchar(cdna_string)-1)
		updateTextInput(session = session,inputId = paste0("cDNA_",i), value = cdna_string)
		}
		if(length(ya$sequence_files[[i]]$find_pattern)==1){
		updateCheckboxInput(session = session, inputId = "patternsearch", value = T)
		updateSelectInput(session = session, inputId = "patternRead", choices = paste("Read",1:length(ya$sequence_files)), selected = paste("Read",i))
		updateTextInput(session = session, inputId = "pattern", value = ya$sequence_files[[i]]$find_pattern)
		}

		}

		@@ -342,7 +413,7 @@ server <- function(input, output, session) {
		updateRadioButtons(session = session, inputId = "barcodeChoice", selected = "Automatic")
		}
		if (!is.null(ya$barcodes$barcode_file)){
		updateRadioButtons(session = session, inputId = "barcodeChoice", selected = "Barcod whitelist")
		updateRadioButtons(session = session, inputId = "barcodeChoice", selected = "Barcode whitelist")
		updateTextInput(session = session, inputId = "BCfile", value = ya$barcodes$barcode_file)
		}
		if (!is.null(ya$barcodes$barcode_num)){

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