inst/extdata/app.R
In caggtaagtat/VarCon: VarCon
#Load ggplot package to render the plots
library("ggplot2")
library("shinycssloaders")
library("shiny")
library("shinyFiles")
library("seqinr")
library("Biostrings")
library("BSgenome")
library("VarCon")
###########################################
## Server and UI code
## Server in and output Skript
server <- function(input, output, session) {
## close the R session when app closes
session$onSessionEnded(function() {
stopApp()
})
## Report when upload of reference genome is complete
output$sum_text2 <- renderUI({
## Genome fasta to download e.g. from
## ftp://ftp.ensembl.org/pub/release-99/fasta/homo_sapiens/
## dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz
referenceDnaStringSet2 <- readDNAStringSet(path$pth, format="fasta",use.names=TRUE)
ref_names <- as.character(lapply(names(referenceDnaStringSet2),
function(x){ strsplit(x, " ")[[1]][[1]]}))
names(referenceDnaStringSet2) <- ref_names
referenceDnaStringSet <<- referenceDnaStringSet2
HTML("Upload of reference genome completed...")
})
## Report when upload of reference genome is complete
output$sum_text22 <- renderUI({
## Get human transcript tables e.g. from https://github.com/caggtaagtat/VarConTables
transCoord <- read.csv(path3$pth3, sep=";")
HTML("Upload of transcript table completed...")
})
## Generate the text for describing the difference between the Hexplorer Scores of both sequences
output$sum_text <- renderUI({
gene2transcript <- read.csv(path2$pth2, sep=";", stringsAsFactors=FALSE)
#Get information about the SNV
res <- getSeqInfoFromVariation(referenceDnaStringSet, input$transcriptID, input$variation,
ntWindow= input$ntWindow, transCoord, gene2transcript=gene2transcript)
#Sum up the info
HTML(paste(paste0("For the given annotation ",res$funcAnnotation,
" within transcript ", res$transcript,
" following sequence was found around the chromosomal coordinate ",
res$genomicCoordinate," on chromosome ",res$chromosome, " :"),
"",paste0("Ref Seq: ",res$sequence),"",
paste0("Ref+vari:",res$altSeq) , sep="<br/>"))
})
## Generate the plot where you can mark the area to zoom in
output$plot <- renderPlot({
gene2transcript <- read.csv(path2$pth2, sep=";", stringsAsFactors=FALSE)
## Retrieve information form genome
res <- getSeqInfoFromVariation(referenceDnaStringSet, input$transcriptID,
input$variation, ntWindow=input$ntWindow, transCoord,
gene2transcript=gene2transcript)
## Calculate HZEI values
durchzahl <- calculateHZEIperNT(res$sequence)
durchzahl$Sequence <- "sequence of interest"
plot <- ggplot(durchzahl, aes(x = durchzahl, y = endhex, fill=Sequence )) +scale_y_continuous(name="Hexplorer score",breaks=c(seq(-75,0,5),seq(2,34,2)),limits=c(min(durchzahl$endhex)-5,max(c(durchzahl$hbs,durchzahl$endhex))+1) )+
scale_fill_manual(values=c("#56B4E9", "#000000"))+
geom_bar(stat='identity', position = "dodge")+ xlab("Sequence")+ylab("Hexplorer score")+
theme(axis.title.x=element_blank(),axis.text.x=element_blank(),axis.ticks.x=element_blank())+
annotate("text", label =substr(durchzahl$seq9[durchzahl$Sequence=="sequence of interest"],6,6 ) , x= 1:((nrow(durchzahl))), y = min(durchzahl$endhex-4), size = 3, colour = "black")
plot
})
## Generate the plot where you can mark the area to zoom in
output$plot2 <- renderPlot({
gene2transcript <- read.csv(path2$pth2, sep=";", stringsAsFactors=FALSE)
## Retrieve information form genome
res <- getSeqInfoFromVariation(referenceDnaStringSet, input$transcriptID,
input$variation, ntWindow=input$ntWindow, transCoord,
gene2transcript=gene2transcript)
generateHEXplorerPlot(res,input$ntWindow)
})
## Create reactive value ranges, for the zooming plot
ranges2 <- reactiveValues(x = NULL)
## Genereate the plot, where you can see a zoomed in version of the plot above
output$plot_zoom <- renderPlot({
gene2transcript <- read.csv(path2$pth2, sep=";", stringsAsFactors=FALSE)
## Retrieve information form genome
res <- getSeqInfoFromVariation(referenceDnaStringSet, input$transcriptID,
input$variation, ntWindow=input$ntWindow,
transCoord,gene2transcript=gene2transcript)
## Calculate HZEI values
durchzahl <- calculateHZEIperNT(res$sequence)
durchzahl$Sequence <- "sequence of interest"
plot <- ggplot(durchzahl, aes(x = durchzahl, y = endhex, fill=Sequence )) +scale_y_continuous(name="Hexplorer score",breaks=c(seq(-75,0,5),seq(2,34,2)),limits=c(min(durchzahl$endhex)-6,max(c(durchzahl$hbs,durchzahl$endhex))+1) )+
scale_fill_manual(values=c("#56B4E9", "#000000"))+
geom_bar(stat='identity', position = "dodge")+ xlab("Sequence")+ylab("Hexplorer score")+
theme(axis.title.x=element_blank(),axis.text.x=element_blank(),axis.ticks.x=element_blank())+
annotate("text", label =substr(durchzahl$seq9[durchzahl$Sequence=="sequence of interest"],6,6 ) , x= 1:((nrow(durchzahl))), y = min(durchzahl$endhex-4), size = 3, colour = "black")+
coord_cartesian(xlim = ranges2$x, expand = FALSE)
plot
})
## Genereate the plot, where you can see a zoomed in version of the plot above
output$plot2_zoom <- renderPlot({
gene2transcript <- read.csv(path2$pth2, sep=";", stringsAsFactors=FALSE)
## Retrieve information form genome
res <- getSeqInfoFromVariation(referenceDnaStringSet, input$transcriptID,
input$variation, ntWindow=input$ntWindow, transCoord,
gene2transcript=gene2transcript)
results_plot <- generateHEXplorerPlot(res,input$ntWindow)
results_plot+coord_cartesian(xlim = ranges2$x, expand = FALSE)
})
## Create a function which keeps checking on the input with the mouse
observe({
brush <- input$plot2_brush
if (!is.null(brush)) {
ranges2$x <- c(brush$xmin, brush$xmax)
} else {
ranges2$x <- NULL
}
})
## Generate the text for describing the difference between the Hexplorer Scores of both sequences
output$plot2_text <- renderUI({
gene2transcript <- read.csv(path2$pth2, sep=";", stringsAsFactors=FALSE)
## Retrieve information form genome
res <- getSeqInfoFromVariation(referenceDnaStringSet, input$transcriptID,
input$variation, ntWindow=input$ntWindow,
transCoord,gene2transcript=gene2transcript)
## calculte HZEI values
durchzahl <- calculateHZEIperNT(res$sequence)
durchzahl$Sequence <- "reference"
durchzahl2 <- calculateHZEIperNT(res$altSeq)
durchzahl2$Sequence <- "alternative"
durchzahl$mut_hex <- durchzahl2$endhex
durchzahl$diff_hex <- durchzahl$mut_hex- durchzahl$endhex
pre <- ""
if(sum(durchzahl$diff_hex) > 0) pre <- "+"
## Return the Difference in the score
HTML(paste0("The difference in the HEXplorer Score integral amounts to ", paste0(pre, sum(durchzahl$diff_hex)), " in total."))
})
## Define reactive paths
path <- reactiveValues(
pth= system.file("extdata", "referenceDnaStringSet.fa", package="VarCon")
)
path2 <- reactiveValues(
pth2= system.file("extdata", "fastaEx.fa", package="Biostrings")
)
path3 <- reactiveValues(
pth3= system.file("extdata", "fastaEx.fa", package="Biostrings")
)
observeEvent(input$filechoose,{
path$pth <- file.choose()
})
observeEvent(input$filechoose2,{
path2$pth2 <- file.choose()
})
observeEvent(input$filechoose3,{
path3$pth3 <- file.choose()
})
}
#User Interface Script
ui <- fluidPage(
## Type Headline
titlePanel("VarCon: Retrieve genomic sequence around sequence variation"),
"VarCon retrieves the surrounding genomic sequence of a stated sequence variation and visualizes potential changes in sequence elements important for splicing. Please first upload the fasta file of the respective reference genome sequence. Loading and processing of the data will take up to 2 minutes.",
br(),
br(),
## Have different tabs in your programm
tabsetPanel(type = "tabs",
tabPanel("Upload reference sequence",
fluidRow(
column(4, h4("Path of fasta reference genome"),
actionButton("filechoose",label = "Path to FASTA file")
),
column(4, h4("Path of transcript table"),
actionButton("filechoose3",label = "Path to transcript table")),
column(3, h4("Path of gene to transcript table"),
actionButton("filechoose2",label = "Path to gene2transcript table")
)
),
fluidRow(
column(4, withSpinner(htmlOutput("sum_text2"), type=6)),
column(4, withSpinner(htmlOutput("sum_text22"), type=6))
)
),
tabPanel("Retrieve sequence around variation",
fluidRow(
column(3,
h4("Please enter the required information"),
helpText("Please enter the transcript of interrest",
"an the annotation of the functional variation."
)),
column(3, textInput("transcriptID", label = h4("Transcript ID (ENSEMBL)"),value= "pseudo_ENST00000650636")),
column(3, textInput("variation", label = h4("Functional variation"),value= "c.412T>G/p.(B89O)")),
column(3, numericInput("ntWindow", label = h4("Seq x nt up/downstream"), value= 20, min=5, max=150))
),
br(),
fluidRow(
column(12, withSpinner(htmlOutput("sum_text"), type=6))
),
br()
),
tabPanel("Impact of variation on splicing sequence elements",
br(),
br(),
withSpinner(plotOutput("plot2", height = 200,
brush = brushOpts(
id = "plot2_brush",
resetOnNew = TRUE
)), type =6),
h4("Zoomed in plot:"),
plotOutput("plot2_zoom", height = 200),
br(),
htmlOutput("plot2_text")
),
tabPanel("Manual",
h3("1. Upload reference genome fasta file"),
"First, please upload the fasta file (or zipped fasta.gz) of the reference genome sequence.",
br(),
"If needed, the required file can be downloaded from the Ensembl ftp server ftp://ftp.ensembl.org/pub/release-99/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz",
br(),
br(),
h3("2. Select genome assembly"),
"Next, select whether the uploaded genome reference file originated from assembly GRCh37 or GRCh38.",
"The respective transcript table, holding the genomic exon coordinates will be selected.",
br(),
br(),
h3("3. Select gene to transcript conversion table (optional)"),
"Select a csv-table holding gene names and gene transcripts which shall be used synonymously during the querries.",
br(),
br(),
h3("4. Data entry"),
"On the next panel, now enter the respective transcript name (or gene name) and the single nucleotide variation of interest.",
"The sequence variations can either refer to the nucleotide positions within the coding sequence or genomic coordiantes.",
"Example variations: c.142+2A>T or g.12746124G>A",
br(),
br()
)
)
)
shinyApp(ui = ui, server = server)
caggtaagtat/VarCon documentation built on Nov. 26, 2020, 7:03 a.m.
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#Load ggplot package to render the plots
library("ggplot2")
library("shinycssloaders")
library("shiny")
library("shinyFiles")
library("seqinr")
library("Biostrings")
library("BSgenome")
library("VarCon")
###########################################
## Server and UI code
## Server in and output Skript
server <- function(input, output, session) {
## close the R session when app closes
session$onSessionEnded(function() {
stopApp()
})
## Report when upload of reference genome is complete
output$sum_text2 <- renderUI({
## Genome fasta to download e.g. from
## ftp://ftp.ensembl.org/pub/release-99/fasta/homo_sapiens/
## dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz
referenceDnaStringSet2 <- readDNAStringSet(path$pth, format="fasta",use.names=TRUE)
ref_names <- as.character(lapply(names(referenceDnaStringSet2),
function(x){ strsplit(x, " ")[[1]][[1]]}))
names(referenceDnaStringSet2) <- ref_names
referenceDnaStringSet <<- referenceDnaStringSet2
HTML("Upload of reference genome completed...")
})
## Report when upload of reference genome is complete
output$sum_text22 <- renderUI({
## Get human transcript tables e.g. from https://github.com/caggtaagtat/VarConTables
transCoord <- read.csv(path3$pth3, sep=";")
HTML("Upload of transcript table completed...")
})
## Generate the text for describing the difference between the Hexplorer Scores of both sequences
output$sum_text <- renderUI({
gene2transcript <- read.csv(path2$pth2, sep=";", stringsAsFactors=FALSE)
#Get information about the SNV
res <- getSeqInfoFromVariation(referenceDnaStringSet, input$transcriptID, input$variation,
ntWindow= input$ntWindow, transCoord, gene2transcript=gene2transcript)
#Sum up the info
HTML(paste(paste0("For the given annotation ",res$funcAnnotation,
" within transcript ", res$transcript,
" following sequence was found around the chromosomal coordinate ",
res$genomicCoordinate," on chromosome ",res$chromosome, " :"),
"",paste0("Ref Seq: ",res$sequence),"",
paste0("Ref+vari:",res$altSeq) , sep="<br/>"))
})
## Generate the plot where you can mark the area to zoom in
output$plot <- renderPlot({
gene2transcript <- read.csv(path2$pth2, sep=";", stringsAsFactors=FALSE)
## Retrieve information form genome
res <- getSeqInfoFromVariation(referenceDnaStringSet, input$transcriptID,
input$variation, ntWindow=input$ntWindow, transCoord,
gene2transcript=gene2transcript)
## Calculate HZEI values
durchzahl <- calculateHZEIperNT(res$sequence)
durchzahl$Sequence <- "sequence of interest"
plot <- ggplot(durchzahl, aes(x = durchzahl, y = endhex, fill=Sequence )) +scale_y_continuous(name="Hexplorer score",breaks=c(seq(-75,0,5),seq(2,34,2)),limits=c(min(durchzahl$endhex)-5,max(c(durchzahl$hbs,durchzahl$endhex))+1) )+
scale_fill_manual(values=c("#56B4E9", "#000000"))+
geom_bar(stat='identity', position = "dodge")+ xlab("Sequence")+ylab("Hexplorer score")+
theme(axis.title.x=element_blank(),axis.text.x=element_blank(),axis.ticks.x=element_blank())+
annotate("text", label =substr(durchzahl$seq9[durchzahl$Sequence=="sequence of interest"],6,6 ) , x= 1:((nrow(durchzahl))), y = min(durchzahl$endhex-4), size = 3, colour = "black")
plot
})
## Generate the plot where you can mark the area to zoom in
output$plot2 <- renderPlot({
gene2transcript <- read.csv(path2$pth2, sep=";", stringsAsFactors=FALSE)
## Retrieve information form genome
res <- getSeqInfoFromVariation(referenceDnaStringSet, input$transcriptID,
input$variation, ntWindow=input$ntWindow, transCoord,
gene2transcript=gene2transcript)
generateHEXplorerPlot(res,input$ntWindow)
})
## Create reactive value ranges, for the zooming plot
ranges2 <- reactiveValues(x = NULL)
## Genereate the plot, where you can see a zoomed in version of the plot above
output$plot_zoom <- renderPlot({
gene2transcript <- read.csv(path2$pth2, sep=";", stringsAsFactors=FALSE)
## Retrieve information form genome
res <- getSeqInfoFromVariation(referenceDnaStringSet, input$transcriptID,
input$variation, ntWindow=input$ntWindow,
transCoord,gene2transcript=gene2transcript)
## Calculate HZEI values
durchzahl <- calculateHZEIperNT(res$sequence)
durchzahl$Sequence <- "sequence of interest"
plot <- ggplot(durchzahl, aes(x = durchzahl, y = endhex, fill=Sequence )) +scale_y_continuous(name="Hexplorer score",breaks=c(seq(-75,0,5),seq(2,34,2)),limits=c(min(durchzahl$endhex)-6,max(c(durchzahl$hbs,durchzahl$endhex))+1) )+
scale_fill_manual(values=c("#56B4E9", "#000000"))+
geom_bar(stat='identity', position = "dodge")+ xlab("Sequence")+ylab("Hexplorer score")+
theme(axis.title.x=element_blank(),axis.text.x=element_blank(),axis.ticks.x=element_blank())+
annotate("text", label =substr(durchzahl$seq9[durchzahl$Sequence=="sequence of interest"],6,6 ) , x= 1:((nrow(durchzahl))), y = min(durchzahl$endhex-4), size = 3, colour = "black")+
coord_cartesian(xlim = ranges2$x, expand = FALSE)
plot
})
## Genereate the plot, where you can see a zoomed in version of the plot above
output$plot2_zoom <- renderPlot({
gene2transcript <- read.csv(path2$pth2, sep=";", stringsAsFactors=FALSE)
## Retrieve information form genome
res <- getSeqInfoFromVariation(referenceDnaStringSet, input$transcriptID,
input$variation, ntWindow=input$ntWindow, transCoord,
gene2transcript=gene2transcript)
results_plot <- generateHEXplorerPlot(res,input$ntWindow)
results_plot+coord_cartesian(xlim = ranges2$x, expand = FALSE)
})
## Create a function which keeps checking on the input with the mouse
observe({
brush <- input$plot2_brush
if (!is.null(brush)) {
ranges2$x <- c(brush$xmin, brush$xmax)
} else {
ranges2$x <- NULL
}
})
## Generate the text for describing the difference between the Hexplorer Scores of both sequences
output$plot2_text <- renderUI({
gene2transcript <- read.csv(path2$pth2, sep=";", stringsAsFactors=FALSE)
## Retrieve information form genome
res <- getSeqInfoFromVariation(referenceDnaStringSet, input$transcriptID,
input$variation, ntWindow=input$ntWindow,
transCoord,gene2transcript=gene2transcript)
## calculte HZEI values
durchzahl <- calculateHZEIperNT(res$sequence)
durchzahl$Sequence <- "reference"
durchzahl2 <- calculateHZEIperNT(res$altSeq)
durchzahl2$Sequence <- "alternative"
durchzahl$mut_hex <- durchzahl2$endhex
durchzahl$diff_hex <- durchzahl$mut_hex- durchzahl$endhex
pre <- ""
if(sum(durchzahl$diff_hex) > 0) pre <- "+"
## Return the Difference in the score
HTML(paste0("The difference in the HEXplorer Score integral amounts to ", paste0(pre, sum(durchzahl$diff_hex)), " in total."))
})
## Define reactive paths
path <- reactiveValues(
pth= system.file("extdata", "referenceDnaStringSet.fa", package="VarCon")
)
path2 <- reactiveValues(
pth2= system.file("extdata", "fastaEx.fa", package="Biostrings")
)
path3 <- reactiveValues(
pth3= system.file("extdata", "fastaEx.fa", package="Biostrings")
)
observeEvent(input$filechoose,{
path$pth <- file.choose()
})
observeEvent(input$filechoose2,{
path2$pth2 <- file.choose()
})
observeEvent(input$filechoose3,{
path3$pth3 <- file.choose()
})
}
#User Interface Script
ui <- fluidPage(
## Type Headline
titlePanel("VarCon: Retrieve genomic sequence around sequence variation"),
"VarCon retrieves the surrounding genomic sequence of a stated sequence variation and visualizes potential changes in sequence elements important for splicing. Please first upload the fasta file of the respective reference genome sequence. Loading and processing of the data will take up to 2 minutes.",
br(),
br(),
## Have different tabs in your programm
tabsetPanel(type = "tabs",
tabPanel("Upload reference sequence",
fluidRow(
column(4, h4("Path of fasta reference genome"),
actionButton("filechoose",label = "Path to FASTA file")
),
column(4, h4("Path of transcript table"),
actionButton("filechoose3",label = "Path to transcript table")),
column(3, h4("Path of gene to transcript table"),
actionButton("filechoose2",label = "Path to gene2transcript table")
)
),
fluidRow(
column(4, withSpinner(htmlOutput("sum_text2"), type=6)),
column(4, withSpinner(htmlOutput("sum_text22"), type=6))
)
),
tabPanel("Retrieve sequence around variation",
fluidRow(
column(3,
h4("Please enter the required information"),
helpText("Please enter the transcript of interrest",
"an the annotation of the functional variation."
)),
column(3, textInput("transcriptID", label = h4("Transcript ID (ENSEMBL)"),value= "pseudo_ENST00000650636")),
column(3, textInput("variation", label = h4("Functional variation"),value= "c.412T>G/p.(B89O)")),
column(3, numericInput("ntWindow", label = h4("Seq x nt up/downstream"), value= 20, min=5, max=150))
),
br(),
fluidRow(
column(12, withSpinner(htmlOutput("sum_text"), type=6))
),
br()
),
tabPanel("Impact of variation on splicing sequence elements",
br(),
br(),
withSpinner(plotOutput("plot2", height = 200,
brush = brushOpts(
id = "plot2_brush",
resetOnNew = TRUE
)), type =6),
h4("Zoomed in plot:"),
plotOutput("plot2_zoom", height = 200),
br(),
htmlOutput("plot2_text")
),
tabPanel("Manual",
h3("1. Upload reference genome fasta file"),
"First, please upload the fasta file (or zipped fasta.gz) of the reference genome sequence.",
br(),
"If needed, the required file can be downloaded from the Ensembl ftp server ftp://ftp.ensembl.org/pub/release-99/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz",
br(),
br(),
h3("2. Select genome assembly"),
"Next, select whether the uploaded genome reference file originated from assembly GRCh37 or GRCh38.",
"The respective transcript table, holding the genomic exon coordinates will be selected.",
br(),
br(),
h3("3. Select gene to transcript conversion table (optional)"),
"Select a csv-table holding gene names and gene transcripts which shall be used synonymously during the querries.",
br(),
br(),
h3("4. Data entry"),
"On the next panel, now enter the respective transcript name (or gene name) and the single nucleotide variation of interest.",
"The sequence variations can either refer to the nucleotide positions within the coding sequence or genomic coordiantes.",
"Example variations: c.142+2A>T or g.12746124G>A",
br(),
br()
)
)
)
shinyApp(ui = ui, server = server)
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