R/ShinySangerAlignmentServer.R
In roblanf/sangeranalyseR: sangeranalyseR: a suite of functions for the analysis of Sanger sequence data in R
Defines functions
SangerAlignmentServer
### ============================================================================
### R shiny SangerAlignment server function
### ============================================================================
SangerAlignmentServer <- function(input, output, session) {
# Suppress Warning
options(warn = -1)
### ------------------------------------------------------------------------
### SangerAlignment parameters initialization.
### ------------------------------------------------------------------------
SangerAlignment <- getShinyOption("sangerAlignment")
shinyDirectory <- getShinyOption("shinyDirectory")
colors <- getShinyOption("colors")
SangerAlignment <- SangerAlignment[[1]]
SangerAlignmentNum <- length(SangerAlignment@contigList)
SangerAlignmentParam <- lapply(seq_len(SangerAlignmentNum), function(i) {
### --------------------------------------------------------------------
### SangerContig-related parameters initialization.
### --------------------------------------------------------------------
# readFeature
SCName <- paste0(i, " Contig")
# Forward & reverse reads list
SangerReadFReadList <-
SangerAlignment@contigList[[i]]@forwardReadList
SangerReadRReadsList <-
SangerAlignment@contigList[[i]]@reverseReadList
forwardReadNum <- length(SangerReadFReadList)
reverseReadNum <- length(SangerReadRReadsList)
# readFeature
forwardReadFeature <- vapply(seq_len(forwardReadNum), function(j)
paste0(j, " ",
SangerReadFReadList[[j]]@readFeature), character(1))
reverseReadFeature <- vapply(seq_len(reverseReadNum), function(j)
paste0(j, " ",
SangerReadRReadsList[[j]]@readFeature), character(1))
SangerReadFeature <- c(forwardReadFeature, reverseReadFeature)
# readFileName (basename)
forwardReadBFN <- vapply(seq_len(forwardReadNum), function(j)
basename(SangerReadFReadList[[j]]@readFileName), character(1))
reverseReadBFN <- vapply(seq_len(reverseReadNum), function(j)
basename(SangerReadRReadsList[[j]]@readFileName), character(1))
SangerReadBFN <- c(forwardReadBFN, reverseReadBFN)
return(list(SCName = SCName,
forwardReadNum = forwardReadNum,
reverseReadNum = reverseReadNum,
forwardReadFeature = forwardReadFeature,
reverseReadFeature = reverseReadFeature,
SangerReadBFN = SangerReadBFN))
})
### ------------------------------------------------------------------------
### SangerAlignment reactiveValue
### ------------------------------------------------------------------------
sangerAlignmentParam <-
reactiveValues(
contigsConsensus = SangerAlignment@contigsConsensus,
contigsAlignment = as.character(SangerAlignment@contigsAlignment),
contigsTree = SangerAlignment@contigsTree)
### ------------------------------------------------------------------------
### SangerContig reactiveValue
### ------------------------------------------------------------------------
contigParam <-
reactiveValues(
contigName = NULL,
contigSeq = NULL,
differencesDF = NULL,
alignment = NULL,
distanceMatrix = NULL,
dendrogram = NULL,
indelsDF = NULL,
stopCodonsDF = NULL,
secondaryPeakDF = NULL)
### ------------------------------------------------------------------------
### SingleRead reactiveValue
### ------------------------------------------------------------------------
sequenceParam <- reactiveValues(primarySeq = "",
secondarySeq = "",
primaryAASeqS1 = "",
primaryAASeqS2 = "",
primaryAASeqS3 = "")
trimmedRV <- reactiveValues(rawSeqLength = 0,
rawMeanQualityScore = 0,
rawMinQualityScore = 0,
trimmedStartPos = 0,
trimmedFinishPos = 0,
trimmedSeqLength = 0,
trimmedMeanQualityScore = 0,
trimmedMinQualityScore = 0,
remainingRatio = 0)
trimmedParam <- reactiveValues(M1TrimmingCutoff = 0,
M2CutoffQualityScore = 0,
M2SlidingWindowSize = 0)
ChromatogramParam <- reactiveValues(baseNumPerRow = 0,
heightPerRow = 0,
signalRatioCutoff = 0,
showTrimmed = TRUE)
############################################################################
### Main panel dynamic UI
############################################################################
output$aligned_contigSeq_content <- renderUI({
sidebar_menu <- tstrsplit(input$sidebar_menu, " ")
if (sidebar_menu[[1]] == "Contigs" &&
sidebar_menu[[2]] == "Alignment" &&
sidebar_menu[[3]] == "Overview" &&
sidebar_menu[[4]] == "Page" &&
sidebar_menu[[5]] == "_" ) {
h1(input$sidebar_menu)
log_info(">>>>>>>> Inside 'Contigs Alignment Overview Page _'")
shinyjs::disable("closeUI")
shinyjs::disable("recalculateButtonSA")
log_info("######## Reactive button clicked !!!")
log_info("######## Start re-aligning contigs")
CSSetResult <-
alignContigs (SangerAlignment@contigList,
SangerAlignment@geneticCode,
SangerAlignment@refAminoAcidSeq,
SangerAlignment@contigList[[1]]@minFractionCall,
SangerAlignment@contigList[[1]]@maxFractionLost,
1)
SangerAlignment@contigsConsensus <<- CSSetResult$consensus
SangerAlignment@contigsAlignment <<- CSSetResult$aln
SangerAlignment@contigsTree <<- CSSetResult$aln.tree
sangerAlignmentParam[["contigsConsensus"]] <<- SangerAlignment@contigsConsensus
sangerAlignmentParam[["contigsAlignment"]] <<- as.character(SangerAlignment@contigsAlignment)
sangerAlignmentParam[["contigsTree"]] <<- SangerAlignment@contigsTree
log_info("######## Finish contigs re-alignment")
shinyjs::enable("recalculateButtonSA")
shinyjs::enable("closeUI")
fluidRow(
useShinyjs(),
box(title = tags$p("Input Parameters: ",
style = "font-size: 26px;
font-weight: bold;"),
solidHeader = TRUE, collapsible = TRUE,
status = "success", width = 12,
tags$hr(style = ("border-top: 0.2px hidden #A9A9A9;")),
fluidRow(
column(width = 12,
actionBttn("recalculateButtonSA",
"Re-calculate Contigs Alignment",
icon = icon("calculator"),
style = "simple", color = "danger",
block = TRUE, size = "lg")
),
column(12,
tags$hr(
style = ("border-top: 2px hidden #A9A9A9;"))
),
column(12,
column(3,
tags$p(tagList(icon("caret-right"),
"Output Directory: "),
style = "font-size: 20px;
font-weight: bold;"),
),
column(9,
h4(shinyDirectory),
)
),
column(12,
column(3,
tags$p(
tagList(icon("caret-right"),
"Raw ABI Parent Directory:"),
style = "font-size: 20px;
font-weight: bold;"),
),
column(9,
h4(SangerAlignment@ABIF_Directory),
)
),
column(12,
column(3,
tags$p(tagList(icon("caret-right"),
"Forward Suffix RegExp: "),
style = "font-size: 20px;
font-weight: bold;"),
),
column(9,
h4(SangerAlignment@REGEX_SuffixForward),
)
),
column(12,
column(3,
tags$p(tagList(icon("caret-right"),
"Reverse Suffix RegExp: "),
style = "font-size: 20px;
font-weight: bold;"),
),
column(9,
h4(SangerAlignment@REGEX_SuffixReverse),
)
),
column(12,
column(3,
tags$p(tagList(icon("caret-right"),
"Contigs Number: "),
style = "font-size: 20px;
font-weight: bold;"),
),
column(9,
h4(length(SangerAlignment@
contigList)),
)
),
tags$hr(style = ("border-top: 4px hidden #A9A9A9;")),
box(title = tags$p("Genetic Code Data Frame",
style = "font-size: 24px;
font-weight: bold;"),
collapsible = TRUE,
status = "success", width = 12,
column(width = 2,
tags$p("Tri-nucleotide:",
style = "font-size: 15px;
font-weight: bold;"),
tags$p("Amino Acid : ",
style = "font-size: 15px;
font-weight: bold;"),
tags$p("('*' : stop codon) ",
style = "font-size: 12px;
font-weight: italic;"),
),
column(width = 10,
excelOutput("geneticCodeDF",
width = "100%", height = "50"),
style = paste("height:100%; ",
"overflow-y: hidden;",
"overflow-x: scroll;")
),
),
uiOutput("SArefAminoAcidSeq") ,
),
),
box(title = tags$p(tagList(icon("dot-circle"),
"SangerAlignment Results: "),
style = "font-size: 26px;
font-weight: bold;"),
solidHeader = TRUE, collapsible = TRUE,
status = "success", width = 12,
tags$hr(style = ("border-top: 4px hidden #A9A9A9;")),
box(title = tags$p("Contigs Alignment",
style = "font-size: 24px;
font-weight: bold;"),
collapsible = TRUE,
status = "success", width = 12,
column(width = 12,
htmlOutput("sangerAlignmentAlignmentHTML"),
),
),
box(title = tags$p("Contigs Tree",
style = "font-size: 24px;
font-weight: bold;"),
collapsible = TRUE,
status = "success", width = 12,
column(width = 12,
# uiOutput("SATreePlotUI"),
plotOutput("SATreePlot"),
style = paste("height:100%; overflow-y:",
"scroll;overflow-x: scroll;")
)
),
),
)
} else if (!is.na(strtoi(sidebar_menu[[1]])) &&
sidebar_menu[[2]] == "Sanger" &&
sidebar_menu[[3]] == "Contig" &&
sidebar_menu[[4]] == "Overview" &&
sidebar_menu[[5]] == "Page") {
contigIndex <- strtoi(sidebar_menu[[1]])
log_info(">>>>>>>> Inside '", input$sidebar_menu, "'")
shinyjs::disable("closeUI")
shinyjs::disable("recalculateButton")
log_info("@@@@@@@ 'Reactive button' has been clicked")
log_info("In the main")
log_info("######## Start recalculating contig")
CSResult<-
calculateContigSeq (
SangerAlignment@contigList[[contigIndex]]@inputSource,
SangerAlignment@contigList[[contigIndex]]@forwardReadList,
SangerAlignment@contigList[[contigIndex]]@reverseReadList,
SangerAlignment@contigList[[contigIndex]]@refAminoAcidSeq,
SangerAlignment@contigList[[contigIndex]]@minFractionCall,
SangerAlignment@contigList[[contigIndex]]@maxFractionLost,
SangerAlignment@contigList[[contigIndex]]@geneticCode,
SangerAlignment@contigList[[contigIndex]]@acceptStopCodons,
SangerAlignment@contigList[[contigIndex]]@readingFrame)
SangerAlignment@contigList[[contigIndex]]@contigSeq <<- CSResult$consensusGapfree
SangerAlignment@contigList[[contigIndex]]@differencesDF <<- CSResult$diffsDf
SangerAlignment@contigList[[contigIndex]]@alignment <<- CSResult$aln2
SangerAlignment@contigList[[contigIndex]]@distanceMatrix <<- CSResult$dist
SangerAlignment@contigList[[contigIndex]]@dendrogram <<- CSResult$dend
SangerAlignment@contigList[[contigIndex]]@indelsDF <<- CSResult$indels
SangerAlignment@contigList[[contigIndex]]@stopCodonsDF <<- CSResult$stopsDf
SangerAlignment@contigList[[contigIndex]]@secondaryPeakDF <<- CSResult$spDf
contigParam[["contigName"]] <<- SangerAlignment@contigList[[contigIndex]]@contigName
contigParam[["contigSeq"]] <<- SangerAlignment@contigList[[contigIndex]]@contigSeq
contigParam[["differencesDF"]] <<- SangerAlignment@contigList[[contigIndex]]@differencesDF
contigParam[["alignment"]] <<- as.character(SangerAlignment@contigList[[contigIndex]]@alignment)
contigParam[["distanceMatrix"]] <<-SangerAlignment@contigList[[contigIndex]]@distanceMatrix
contigParam[["dendrogram"]] <<- SangerAlignment@contigList[[contigIndex]]@dendrogram
contigParam[["indelsDF"]] <<- SangerAlignment@contigList[[contigIndex]]@indelsDF
contigParam[["stopCodonsDF"]] <<- SangerAlignment@contigList[[contigIndex]]@stopCodonsDF
contigParam[["secondaryPeakDF"]] <<- SangerAlignment@contigList[[contigIndex]]@secondaryPeakDF
log_info("######## Finish recalculating contig")
shinyjs::enable("recalculateButton")
shinyjs::enable("closeUI")
fluidRow(
useShinyjs(),
box(title = tags$p(tagList(icon("dot-circle"),
"Basic Information: "),
style = "font-size: 26px;
font-weight: bold;"),
solidHeader = TRUE, collapsible = TRUE,
status = "success", width = 12,
tags$hr(
style = ("border-top: 0.2px hidden #A9A9A9;")),
fluidRow(
column(width = 12,
actionBttn("recalculateButton",
"Re-calculate Contig",
icon = icon("calculator"),
style = "simple",
color = "danger",
block = TRUE, size = "lg")
),
column(12,
tags$hr(
style = ("border-top: 2px
hidden #A9A9A9;")),
),
column(12,
column(3,
tags$p(tagList(icon("caret-right"),
"Output Directory:"),
style = "font-size: 20px;
font-weight: bold;"),
),
column(9,
h4(shinyDirectory),
)
),
column(12,
column(3,
tags$p(
tagList(icon("caret-right"),
"Raw ABI Parent Directory: "),
style = "font-size: 20px;
font-weight: bold;"),
),
column(9,
h4(SangerAlignment@
ABIF_Directory),
)
),
column(12,
column(3,
tags$p(
tagList(icon("caret-right"),
"Consenesus Read Name:"),
style = "font-size: 20px;
font-weight: bold;"),
),
column(9,
h4(contigParam[["contigName"]]),
)
),
column(12,
column(3,
tags$p(
tagList(icon("caret-right"),
"Forward Suffix RegExp:"),
style = "font-size: 20px;
font-weight: bold;"),
),
column(9,
h4(SangerAlignment@
REGEX_SuffixForward),
)
),
column(12,
column(3,
tags$p(
tagList(icon("caret-right"),
"Forward Read Number:"),
style = "font-size: 20px;
font-weight: bold;"),
),
column(9,
h4(length(SangerAlignment@
contigList[[contigIndex]]@
forwardReadList)),
)
),
column(12,
column(3,
tags$p(
tagList(icon("caret-right"),
"Reverse Suffix RegExp:"),
style = "font-size: 20px;
font-weight: bold;"),
),
column(9,
h4(SangerAlignment@
REGEX_SuffixReverse),
)
),
column(12,
column(3,
tags$p(
tagList(icon("caret-right"),
"Reverse Read Number:"),
style = "font-size: 20px;
font-weight: bold;"),
),
column(9,
h4(length(SangerAlignment@
contigList[[contigIndex]]@
reverseReadList)),
)
),
),
################################################
#### Add this after having reference sample ####
################################################
tags$hr(style = ("border-top: 4px hidden #A9A9A9;")),
box(title = tags$p("Contig Parameters",
style = "font-size: 24px;
font-weight: bold;"),
collapsible = TRUE,
status = "success", width = 12,
column(4,
uiOutput("SAMinReadsNum") ,
),
column(4,
uiOutput("SAMinReadLength") ,
),
column(4,
uiOutput("SAMinFractionCall") ,
),
column(4,
uiOutput("SAMaxFractionLost") ,
),
column(4,
uiOutput("SAAcceptStopCodons") ,
),
column(4,
uiOutput("SAReadingFrame") ,
),
),
box(title = tags$p("Genetic Code Data Frame",
style = "font-size: 24px;
font-weight: bold;"),
collapsible = TRUE,
status = "success", width = 12,
column(width = 2,
tags$p("Tri-nucleotide:",
style = "font-size: 15px;
font-weight: bold;"),
tags$p("Amino Acid : ",
style = "font-size: 15px;
font-weight: bold;"),
tags$p("('*' : stop codon) ",
style = "font-size: 12px;
font-weight: italic;"),
),
column(width = 10,
excelOutput("geneticCodeDF",
width = "100%",
height = "50"),
style = paste("height:100%; ",
"overflow-y: hidden;",
"overflow-x: scroll;")
),
),
uiOutput("SArefAminoAcidSeq") ,
),
box(title = tags$p(tagList(icon("dot-circle"),
"Consensus Read Results: "),
style = "font-size: 26px;
font-weight: bold;"),
solidHeader = TRUE, collapsible = TRUE,
status = "success", width = 12,
tags$hr(style =("border-top: 4px hidden #A9A9A9;")),
box(title = tags$p("Alignment",
style = "font-size: 24px;
font-weight: bold;"),
collapsible = TRUE,
status = "success", width = 12,
column(width = 12,
htmlOutput("contigAlignmentHTML"),
),
),
box(title = tags$p("Differences Data frame",
style = "font-size: 24px;
font-weight: bold;"),
collapsible = TRUE,
status = "success", width = 12,
column(width = 12,
# uiOutput("SADifferencesDFUI"),
dataTableOutput("SADifferencesDF"),
style =
paste("height:100%; overflow-y:",
"scroll;overflow-x: scroll;")
)
),
box(title = tags$p("Dendrogram",
style = "font-size: 24px;
font-weight: bold;"),
collapsible = TRUE,
status = "success", width = 12,
column(width = 12,
plotOutput("dendrogramPlot"),
style =
paste("height:100%; overflow-y:",
"scroll;overflow-x: scroll;")
),
column(width = 12,
tags$hr(
style =("border-top: 4px hidden #A9A9A9;")),
),
column(width = 12,
dataTableOutput("dendrogramDF"),
style =
paste("height:100%; overflow-y:",
"scroll;overflow-x: scroll;")
)
),
box(title = tags$p("Samples Distance",
style = "font-size: 24px;
font-weight: bold;"),
collapsible = TRUE,
status = "success", width = 12,
column(width = 12,
# plot()
# uiOutput("SADistanceMatrixPlotUI"),
plotlyOutput("SADistanceMatrixPlot"),
style =
paste("height:100%; overflow-y:",
"scroll;overflow-x: scroll;")
),
column(width = 12,
tags$hr(
style =("border-top: 4px hidden #A9A9A9;")),
),
column(width = 12,
# uiOutput("SADistanceMatrixUI"),
dataTableOutput("SADistanceMatrix"),
style =
paste("height:100%; overflow-y:",
"scroll;overflow-x: scroll;")
)
),
box(title = tags$p("Indels Data frame",
style = "font-size: 24px;
font-weight: bold;"),
collapsible = TRUE,
status = "success", width = 12,
column(width = 12,
# uiOutput("SAIndelsDFUI"),
dataTableOutput("SAIndelsDF"),
style =
paste("height:100%; overflow-y:",
"scroll;overflow-x: scroll;")
)
),
box(title = tags$p("Stop Codons Data frame",
style = "font-size: 24px;
font-weight: bold;"),
collapsible = TRUE,
status = "success", width = 12,
column(width = 12,
# uiOutput("SAStopCodonsDFUI"),
dataTableOutput("SAStopCodonsDF"),
style =
paste("height:100%; overflow-y:",
"scroll;overflow-x: scroll;")
)
)
)
)
} else if (!is.na(strtoi(sidebar_menu[[1]])) &&
sidebar_menu[[2]] == "Contig" &&
sidebar_menu[[3]] == "-" &&
!is.na(strtoi(sidebar_menu[[4]])) &&
(sidebar_menu[[5]] == "Forward" ||
sidebar_menu[[5]] == "Reverse") &&
sidebar_menu[[6]] == "Read") {
contigIndex <- strtoi(sidebar_menu[[1]])
readIndex <- strtoi(sidebar_menu[[4]])
directionParam <- sidebar_menu[[5]]
if (directionParam == "Forward") {
sequenceParam[["primarySeq"]] <<-
as.character(SangerAlignment@
contigList[[contigIndex]]@
forwardReadList[[readIndex]]@primarySeq)
sequenceParam[["secondarySeq"]] <<-
as.character(SangerAlignment@
contigList[[contigIndex]]@
forwardReadList[[readIndex]]@secondarySeq)
sequenceParam[["primaryAASeqS1"]] <<-
as.character(SangerAlignment@
contigList[[contigIndex]]@
forwardReadList[[readIndex]]@primaryAASeqS1)
sequenceParam[["primaryAASeqS2"]] <<-
as.character(SangerAlignment@
contigList[[contigIndex]]@
forwardReadList[[readIndex]]@primaryAASeqS2)
sequenceParam[["primaryAASeqS3"]] <<-
as.character(SangerAlignment@
contigList[[contigIndex]]@
forwardReadList[[readIndex]]@primaryAASeqS3)
trimmedParam[["M1TrimmingCutoff"]] <<-
SangerAlignment@
contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@
M1TrimmingCutoff
trimmedParam[["M2CutoffQualityScore"]] <<-
SangerAlignment@
contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@
M2CutoffQualityScore
trimmedParam[["M2SlidingWindowSize"]] <<-
SangerAlignment@
contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@
M2SlidingWindowSize
trimmedRV[["rawSeqLength"]] <<-
SangerAlignment@
contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@rawSeqLength
trimmedRV[["rawMeanQualityScore"]] <<-
SangerAlignment@
contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@
rawMeanQualityScore
trimmedRV[["rawMinQualityScore"]] <<-
SangerAlignment@
contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@rawMinQualityScore
trimmedRV[["trimmedStartPos"]] <<-
SangerAlignment@
contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@trimmedStartPos
trimmedRV[["trimmedFinishPos"]] <<-
SangerAlignment@
contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@trimmedFinishPos
trimmedRV[["trimmedSeqLength"]] <<-
SangerAlignment@
contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@trimmedSeqLength
trimmedRV[["trimmedMeanQualityScore"]] <<-
SangerAlignment@
contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@
trimmedMeanQualityScore
trimmedRV[["trimmedMinQualityScore"]] <<-
SangerAlignment@
contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@
trimmedMinQualityScore
trimmedRV[["remainingRatio"]] <<-
round(SangerAlignment@
contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@
remainingRatio * 100, 2)
ChromatogramParam[["baseNumPerRow"]] <<-
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@ChromatogramParam@
baseNumPerRow
ChromatogramParam[["heightPerRow"]] <<-
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@ChromatogramParam@
heightPerRow
ChromatogramParam[["signalRatioCutoff"]] <<-
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@ChromatogramParam@
signalRatioCutoff
ChromatogramParam[["showTrimmed"]] <<-
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@ChromatogramParam@
showTrimmed
SangerReadBFN <-
basename(SangerAlignment@
contigList[[contigIndex]]@
forwardReadList[[readIndex]]@readFileName)
SangerReadAFN <-
SangerAlignment@
contigList[[contigIndex]]@
forwardReadList[[readIndex]]@readFileName
} else if (directionParam == "Reverse") {
sequenceParam[["primarySeq"]] <<-
as.character(SangerAlignment@
contigList[[contigIndex]]@
reverseReadList[[readIndex]]@primarySeq)
sequenceParam[["secondarySeq"]] <<-
as.character(SangerAlignment@
contigList[[contigIndex]]@
reverseReadList[[readIndex]]@secondarySeq)
sequenceParam[["primaryAASeqS1"]] <<-
as.character(SangerAlignment@
contigList[[contigIndex]]@
reverseReadList[[readIndex]]@primaryAASeqS1)
sequenceParam[["primaryAASeqS2"]] <<-
as.character(SangerAlignment@
contigList[[contigIndex]]@
reverseReadList[[readIndex]]@primaryAASeqS2)
sequenceParam[["primaryAASeqS3"]] <<-
as.character(SangerAlignment@
contigList[[contigIndex]]@
reverseReadList[[readIndex]]@primaryAASeqS3)
trimmedParam[["M1TrimmingCutoff"]] <<-
SangerAlignment@
contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@
M1TrimmingCutoff
trimmedParam[["M2CutoffQualityScore"]] <<-
SangerAlignment@
contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@
M2CutoffQualityScore
trimmedParam[["M2SlidingWindowSize"]] <<-
SangerAlignment@
contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@
M2SlidingWindowSize
trimmedRV[["rawSeqLength"]] <<-
SangerAlignment@
contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@rawSeqLength
trimmedRV[["rawMeanQualityScore"]] <<-
SangerAlignment@
contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@
rawMeanQualityScore
trimmedRV[["rawMinQualityScore"]] <<-
SangerAlignment@
contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@rawMinQualityScore
trimmedRV[["trimmedStartPos"]] <<-
SangerAlignment@
contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@trimmedStartPos
trimmedRV[["trimmedFinishPos"]] <<-
SangerAlignment@
contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@trimmedFinishPos
trimmedRV[["trimmedSeqLength"]] <<-
SangerAlignment@
contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@trimmedSeqLength
trimmedRV[["trimmedMeanQualityScore"]] <<-
SangerAlignment@
contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@
trimmedMeanQualityScore
trimmedRV[["trimmedMinQualityScore"]] <<-
SangerAlignment@
contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@
trimmedMinQualityScore
trimmedRV[["remainingRatio"]] <<-
round(SangerAlignment@
contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@
remainingRatio * 100, 2)
ChromatogramParam[["baseNumPerRow"]] <<-
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@ChromatogramParam@
baseNumPerRow
ChromatogramParam[["heightPerRow"]] <<-
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@ChromatogramParam@
heightPerRow
ChromatogramParam[["signalRatioCutoff"]] <<-
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@ChromatogramParam@
signalRatioCutoff
ChromatogramParam[["showTrimmed"]] <<-
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@ChromatogramParam@
showTrimmed
SangerReadBFN <-
basename(SangerAlignment@
contigList[[contigIndex]]@
reverseReadList[[readIndex]]@readFileName)
SangerReadAFN <-
SangerAlignment@
contigList[[contigIndex]]@
reverseReadList[[readIndex]]@readFileName
}
log_info(">>>>>>>> Inside '", input$sidebar_menu, "'")
h1(input$sidebar_menu)
fluidRow(
useShinyjs(),
box(title = tags$p(tagList(icon("dot-circle"),
"Raw File: "),
style = "font-size: 26px;
font-weight: bold;"),
solidHeader = TRUE,
status = "success", width = 12,
h1(SangerReadBFN),
tags$h5(paste("( full path:",
SangerReadAFN,
")"), style = "font-style:italic")),
box(title = tags$p(
tagList(icon("dot-circle"),
"Primary, Secondary DNA Sequences & Amino Acid Sequence (Before Trimming):"),
style = "font-size: 26px;
font-weight: bold;"),
solidHeader = TRUE, collapsible = TRUE,
status = "success", width = 12,
tags$hr(style = ("border-top: 4px hidden #A9A9A9;")),
column(width = 12,
tags$p(tagList(icon("bars"),
"Primary Sequence"),
style = "font-size: 22px;
font-weight: bold;"),
excelOutput("primarySeqDF",
width = "100%", height = "50"),
tags$br(),
tags$br(),
tags$p(tagList(icon("bars"),
"Secondary Sequence"),
style = "font-size: 22px;
font-weight: bold;"),
excelOutput("secondSeqDF",
width = "100%", height = "50"),
tags$br(),
tags$br(),
tags$p(tagList(icon("bars"),
"Quality Phred Score"),
style = "font-size: 22px;
font-weight: bold;"),
excelOutput("qualityScoreDF",
width = "100%", height = "50"),
style = paste("overflow-y: hidden;",
"overflow-x: scroll;")
),
),
box(title = tags$p(tagList(icon("dot-circle"),
"Quality Report: "),
style = "font-size: 26px;
font-weight: bold;"),
solidHeader = TRUE, collapsible = TRUE,
status = "success", width = 12,
tags$hr(
style = ("border-top: 4px hidden #A9A9A9;")),
box(title =
tags$p(tagList(icon("arrow-circle-right"),
"Trimming Parameters Input"),
style = "font-size: 24px;
font-weight: bold;"),
collapsible = TRUE,
status = "success", width = 12,
fluidRow(
column(width = 12,
uiOutput("TrimmingMethodSelectionOutput"),
),
),
column(width = 12,
uiOutput("TrimmingMethodUI"),
),
actionBttn("startTrimmingButton",
"Apply Trimming Parameters",
style = "simple", color = "danger",
block = TRUE, size = "lg")
),
box(title = tags$p(tagList(icon("arrow-circle-left"),
"Trimmed Result Output"),
style = "font-size: 24px;
font-weight: bold;"),
collapsible = TRUE,
status = "success", width = 12,
fluidRow(
box(title = tags$p("Before Trimming",
style = "font-size: 21px;
font-weight: bold;"),
collapsible = TRUE,
status = "success", width = 12,
column(width = 12,
column(4,
uiOutput("rawSeqLength") ,
),
column(4,
uiOutput("rawMeanQualityScore"),
),
column(4,
uiOutput("rawMinQualityScore"),
),
),
),
),
fluidRow(
box(title = tags$p("After Trimming",
style = "font-size: 21px;
font-weight: bold;"),
collapsible = TRUE,
status = "success", width = 12,
column(width = 12,
column(4,
uiOutput("trimmedSeqLength"),
),
column(4,
uiOutput("trimmedMeanQualityScore"),
),
column(4,
uiOutput("trimmedMinQualityScore"),
),
),
column(width = 12,
column(4,
uiOutput("trimmedStartPos") ,
),
column(4,
uiOutput("trimmedFinishPos") ,
),
column(4,
uiOutput("remainingRatio") ,
)
),
),
),
tags$hr(
style = ("border-top: 6px double #A9A9A9;")),
fluidRow(
box(title = tags$p("Quality Trimming Plot",
style = "font-size: 21px;
font-weight: bold;"),
collapsible = TRUE,
status = "success", width = 12,
plotlyOutput("qualityQualityBasePlot") %>%
withSpinner()),
),
),
),
box(title =
tags$p(tagList(icon("dot-circle"),
"DNA Sequence
(After Trimming):"),
style = "font-size: 26px;
font-weight: bold;"),
solidHeader = TRUE, collapsible = TRUE,
status = "success", width = 12,
tags$hr(style = ("border-top: 4px hidden #A9A9A9;")),
column(width = 12,
tags$p(tagList(icon("bars"),
"Primary Sequence"),
style = "font-size: 22px;
font-weight: bold;"),
excelOutput("primarySeqTrimmedDF",
width = "100%", height = "50"),
tags$br(),
tags$br(),
tags$p(tagList(icon("bars"),
"Secondary Sequence"),
style = "font-size: 22px;
font-weight: bold;"),
excelOutput("secondSeqTrimmedDF",
width = "100%", height = "50"),
tags$br(),
tags$br(),
tags$p(tagList(icon("bars"),
"Quality Phred Score"),
style = "font-size: 22px;
font-weight: bold;"),
excelOutput("qualityScoreTrimmedDF",
width = "100%", height = "50"),
tags$br(),
tags$br(),
tags$p(tagList(icon("bars"),
"AA Sequence 1"),
style = "font-size: 22px;
font-weight: bold;"),
excelOutput("PrimAASeqS1DF",
width = "100%", height = "50"),
tags$br(),
tags$br(),
tags$p(tagList(icon("bars"),
"AA Sequence 2"),
style = "font-size: 22px;
font-weight: bold;"),
excelOutput("PrimAASeqS2DF",
width = "100%", height = "50"),
tags$br(),
tags$br(),
tags$p(tagList(icon("bars"),
"AA Sequence 3"),
style = "font-size: 22px;
font-weight: bold;"),
excelOutput("PrimAASeqS3DF",
width = "100%", height = "50"),
style = paste("overflow-y: hidden;",
"overflow-x: scroll;")
)
),
box(title = tags$p(tagList(icon("dot-circle"),
"Chromatogram: "),
style = "font-size: 26px;
font-weight: bold;"),
solidHeader = TRUE, collapsible = TRUE,
status = "success", width = 12,
tags$hr(style = ("border-top: 4px hidden #A9A9A9;")),
box(title = tags$p(tagList(icon("arrow-circle-right"),
"Chromatogram Input"),
style = "font-size: 24px;
font-weight: bold;"),
collapsible = TRUE,
status = "success", width = 12,
column(3,
sliderInput("ChromatogramBasePerRow",
label = h4("Base Number Per Row"),
min = 5,
max = 200,
value = ChromatogramParam[["baseNumPerRow"]]),
sliderInput("ChromatogramHeightPerRow",
label = h4("Height Per Row"),
min = 50,
max = 600,
value =ChromatogramParam[["heightPerRow"]]),
),
column(3,
numericInput(
"ChromatogramSignalRatioCutoff",
h3("Signal Ratio Cutoff"),
value = ChromatogramParam[["signalRatioCutoff"]]),
checkboxInput(
"ChromatogramCheckShowTrimmed",
"Show trimmed region",
value = ChromatogramParam[["showTrimmed"]])
),
column(3,
uiOutput("ChromatogramtrimmedStartPos"),
),
column(3,
uiOutput("ChromatogramtrimmedFinishPos"),
),
actionBttn("saveChromatogramParam",
"Apply Chromatogram Parameters",
style = "simple", color = "danger",
block = TRUE, size = "lg")
),
box(title = tags$p(tagList(icon("arrow-circle-left"),
"Chromatogram Output"),
style = "font-size: 24px;
font-weight: bold;"),
collapsible = TRUE,
status = "success", width = 12,
column(width = 12,
uiOutput("chromatogramUIOutput"),
)
),
)
)
}
})
############################################################################
### All other features (dynamic header / button save / button close)
############################################################################
observeEvent(input$sidebar_menu, {
sidebar_menu <- tstrsplit(input$sidebar_menu, " ")
if (sidebar_menu[[1]] == "Contigs" &&
sidebar_menu[[2]] == "Alignment" &&
sidebar_menu[[3]] == "Overview" &&
sidebar_menu[[4]] == "Page" &&
sidebar_menu[[5]] == "_") {
shinyjs::html("rightHeader", "SangerAlignment Overview Page")
} else if (!is.na(strtoi(sidebar_menu[[1]])) &&
sidebar_menu[[2]] == "Sanger" &&
sidebar_menu[[3]] == "Contig" &&
sidebar_menu[[4]] == "Overview" &&
sidebar_menu[[5]] == "Page") {
contigIndex <- strtoi(sidebar_menu[[1]])
shinyjs::html("rightHeader", paste(contigIndex, "SangerContig Overview Page"))
} else if (!is.na(strtoi(sidebar_menu[[1]])) &&
sidebar_menu[[2]] == "Contig" &&
sidebar_menu[[3]] == "-" &&
!is.na(strtoi(sidebar_menu[[4]])) &&
(sidebar_menu[[5]] == "Forward" ||
sidebar_menu[[5]] == "Reverse") &&
sidebar_menu[[6]] == "Read") {
contigIndex <- strtoi(sidebar_menu[[1]])
readIndex <- strtoi(sidebar_menu[[4]])
directionParam <- sidebar_menu[[5]]
shinyjs::html("rightHeader",
paste(contigIndex, "SangerContig -",
readIndex, directionParam,
"SangerRead", "Page"))
}
})
### ------------------------------------------------------------------------
### observeEvent: Adding dynamic sidebar
### ------------------------------------------------------------------------
# !!! Fix !!!
dynamicMenuSideBarSA(input, output, session, SangerAlignmentParam)
############################################################################
### All other features (dynamic header / button save / button close)
############################################################################
### ------------------------------------------------------------------------
### observeEvent: Button Close UI
### ------------------------------------------------------------------------
observeEvent(input$closeUI, {
log_info("@@@@@@@ 'close button' has been clicked")
btn <- input$closeUI
stopApp()
})
### ------------------------------------------------------------------------
### observeEvent: Button Save S4 object
### ------------------------------------------------------------------------
observeEvent(input$saveS4, {
shinyjs::disable("closeUI")
shinyjs::disable("saveS4")
log_info("@@@@@@@ 'save button' has been clicked")
newS4Object <- file.path(shinyDirectory,
"SangerAlignment.Rda")
showNotification(
ui = column(12,
tags$p(tagList(icon("dot-circle"),
"New S4 object is store as: "),
style = "font-size: 28px;
font-weight: bold;"),
tags$p(paste0("'", newS4Object, "'"),
style = "font-size: 26px;
font-style: italic"),
tags$br(),
tags$p(">> Run",
style = "font-size: 18px;
font-style: italic"),
tags$p(paste0("readRDS(\"",newS4Object,
"\")"),
style = "font-size: 18px;
font-weight: bold;
font-family: Courier, Monospace;"),
tags$p(" to load saved S4 object into R
environment",
style = "font-size: 18px;
font-style: italic")),
closeButton = TRUE, id = "saveNotification",
type = "message", duration = 10)
### --------------------------------------------------------------------
### Save SangerContig quality S4 object
### --------------------------------------------------------------------
saveRDS(SangerAlignment, file=newS4Object)
log_info("New S4 object is store as: ", newS4Object)
NEW_SANGER_ALIGNED_CONSENSUS_READ_SET <<- readRDS(file=newS4Object)
shinyjs::enable("saveS4")
shinyjs::enable("closeUI")
})
### ------------------------------------------------------------------------
### observeEvent: Button contigs alignment re-calculating (SA) UI
### ------------------------------------------------------------------------
observeEvent(input$recalculateButtonSA, {
shinyjs::disable("closeUI")
shinyjs::disable("recalculateButtonSA")
log_info("######## Reactive button clicked !!!")
log_info("######## Start re-aligning contigs")
if (input$sidebar_menu == "Contigs Alignment Overview Page _") {
CSSetResult <-
alignContigs (SangerAlignment@contigList,
SangerAlignment@geneticCode,
SangerAlignment@refAminoAcidSeq,
SangerAlignment@contigList[[1]]@minFractionCall,
SangerAlignment@contigList[[1]]@maxFractionLost,
1)
SangerAlignment@contigsConsensus <<- CSSetResult$consensus
SangerAlignment@contigsAlignment <<- CSSetResult$aln
SangerAlignment@contigsTree <<- CSSetResult$aln.tree
sangerAlignmentParam[["contigsConsensus"]] <<- SangerAlignment@contigsConsensus
sangerAlignmentParam[["contigsAlignment"]] <<- as.character(SangerAlignment@contigsAlignment)
sangerAlignmentParam[["contigsTree"]] <<- SangerAlignment@contigsTree
log_info("######## Finish contigs re-alignment")
}
shinyjs::enable("recalculateButtonSA")
shinyjs::enable("closeUI")
})
### ------------------------------------------------------------------------
### observeEvent: Button SangerContig re-calculating (SA) UI
### ------------------------------------------------------------------------
observeEvent(input$recalculateButton, {
shinyjs::disable("closeUI")
shinyjs::disable("recalculateButton")
log_info("@@@@@@@ 'Reactive button' has been clicked")
log_info("######## Start recalculating contig")
sidebar_menu <- tstrsplit(input$sidebar_menu, " ")
contigIndex <- strtoi(sidebar_menu[[1]])
if (!is.na(contigIndex)) {
CSResult<-
calculateContigSeq (
SangerAlignment@contigList[[contigIndex]]@inputSource,
SangerAlignment@contigList[[contigIndex]]@forwardReadList,
SangerAlignment@contigList[[contigIndex]]@reverseReadList,
SangerAlignment@contigList[[contigIndex]]@refAminoAcidSeq,
SangerAlignment@contigList[[contigIndex]]@minFractionCall,
SangerAlignment@contigList[[contigIndex]]@maxFractionLost,
SangerAlignment@contigList[[contigIndex]]@geneticCode,
SangerAlignment@contigList[[contigIndex]]@acceptStopCodons,
SangerAlignment@contigList[[contigIndex]]@readingFrame)
SangerAlignment@contigList[[contigIndex]]@contigSeq <<- CSResult$consensusGapfree
SangerAlignment@contigList[[contigIndex]]@differencesDF <<- CSResult$diffsDf
SangerAlignment@contigList[[contigIndex]]@alignment <<- CSResult$aln2
SangerAlignment@contigList[[contigIndex]]@distanceMatrix <<- CSResult$dist
SangerAlignment@contigList[[contigIndex]]@dendrogram <<- CSResult$dend
SangerAlignment@contigList[[contigIndex]]@indelsDF <<- CSResult$indels
SangerAlignment@contigList[[contigIndex]]@stopCodonsDF <<- CSResult$stopsDf
SangerAlignment@contigList[[contigIndex]]@secondaryPeakDF <<- CSResult$spDf
contigParam[["contigSeq"]] <<- SangerAlignment@contigList[[contigIndex]]@contigSeq
contigParam[["differencesDF"]] <<- SangerAlignment@contigList[[contigIndex]]@differencesDF
contigParam[["alignment"]] <<- as.character(SangerAlignment@contigList[[contigIndex]]@alignment)
contigParam[["distanceMatrix"]] <<-SangerAlignment@contigList[[contigIndex]]@distanceMatrix
contigParam[["dendrogram"]] <<- SangerAlignment@contigList[[contigIndex]]@dendrogram
contigParam[["indelsDF"]] <<- SangerAlignment@contigList[[contigIndex]]@indelsDF
contigParam[["stopCodonsDF"]] <<- SangerAlignment@contigList[[contigIndex]]@stopCodonsDF
contigParam[["secondaryPeakDF"]] <<- SangerAlignment@contigList[[contigIndex]]@secondaryPeakDF
}
log_info("######## Finish recalculating contig")
shinyjs::enable("recalculateButton")
shinyjs::enable("closeUI")
})
### ------------------------------------------------------------------------
### observeEvent: Button apply trimming parameters
### ------------------------------------------------------------------------
observeEvent(input$startTrimmingButton, {
sidebar_menu <- tstrsplit(input$sidebar_menu, " ")
contigIndex <- strtoi(sidebar_menu[[1]])
readIndex <- strtoi(sidebar_menu[[4]])
directionParam <- sidebar_menu[[5]]
if (!is.na(contigIndex) &&
!is.na(readIndex)) {
if (directionParam == "Forward") {
activated_read_list <- SangerAlignment@contigList[[contigIndex]]@forwardReadList
} else if (directionParam == "Reverse") {
activated_read_list <- SangerAlignment@contigList[[contigIndex]]@reverseReadList
}
if (activated_read_list[[readIndex]]@QualityReport@TrimmingMethod == "M1") {
if (!is.na(as.numeric(input$M1TrimmingCutoffText)) &&
as.numeric(input$M1TrimmingCutoffText) > 0 &&
as.numeric(input$M1TrimmingCutoffText) <= 1) {
inputM1TrimmingCutoffText <- input$M1TrimmingCutoffText
} else {
inputM1TrimmingCutoffText <- 0.0001
}
if (directionParam == "Forward") {
trimmingPos <-
M1inside_calculate_trimming(
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@
qualityPhredScores,
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@
qualityBaseScores,
as.numeric(inputM1TrimmingCutoffText))
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@
M1TrimmingCutoff <<- as.numeric(inputM1TrimmingCutoffText)
trimmedParam[["M1TrimmingCutoff"]] <<-
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@M1TrimmingCutoff
} else if (directionParam == "Reverse") {
trimmingPos <-
M1inside_calculate_trimming(
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@
qualityPhredScores,
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@
qualityBaseScores,
as.numeric(inputM1TrimmingCutoffText))
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@
M1TrimmingCutoff <<- as.numeric(inputM1TrimmingCutoffText)
trimmedParam[["M1TrimmingCutoff"]] <<-
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@M1TrimmingCutoff
}
} else if (activated_read_list[[readIndex]]@QualityReport@TrimmingMethod == "M2") {
if (!is.na(strtoi(input$M2CutoffQualityScoreText)) &&
strtoi(input$M2CutoffQualityScoreText) > 0 &&
strtoi(input$M2CutoffQualityScoreText) <= 60 &&
strtoi(input$M2CutoffQualityScoreText) %% 1 ==0) {
inputM2CutoffQualityScoreText <- input$M2CutoffQualityScoreText
} else {
inputM2CutoffQualityScoreText <- 20
}
if (!is.na(strtoi(input$M2SlidingWindowSizeText)) &&
strtoi(input$M2SlidingWindowSizeText) > 0 &&
strtoi(input$M2SlidingWindowSizeText) <= 40 &&
strtoi(input$M2SlidingWindowSizeText) %% 1 ==0) {
inputM2SlidingWindowSizeText <- input$M2SlidingWindowSizeText
} else {
inputM2SlidingWindowSizeText <- 10
}
if (directionParam == "Forward") {
trimmingPos <-
M2inside_calculate_trimming(
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@
qualityPhredScores,
strtoi(inputM2CutoffQualityScoreText),
strtoi(inputM2SlidingWindowSizeText)
)
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@
M2CutoffQualityScore <<- strtoi(inputM2CutoffQualityScoreText)
trimmedParam[["M2CutoffQualityScore"]] <<-
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@
M2CutoffQualityScore
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@
M2SlidingWindowSize <<- strtoi(inputM2SlidingWindowSizeText)
trimmedParam[["M2SlidingWindowSize"]] <<-
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@
M2SlidingWindowSize
} else if ("Reverse") {
trimmingPos <-
M2inside_calculate_trimming(
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@
qualityPhredScores,
strtoi(inputM2CutoffQualityScoreText),
strtoi(inputM2SlidingWindowSizeText)
)
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@
M2CutoffQualityScore <<- strtoi(inputM2CutoffQualityScoreText)
trimmedParam[["M2CutoffQualityScore"]] <<-
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@
M2CutoffQualityScore
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@
M2SlidingWindowSize <<- strtoi(inputM2SlidingWindowSizeText)
trimmedParam[["M2SlidingWindowSize"]] <<-
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@
M2SlidingWindowSize
}
}
if (directionParam == "Forward") {
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@
rawSeqLength <<- trimmingPos[["rawSeqLength"]]
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@
rawMeanQualityScore <<- trimmingPos[["rawMeanQualityScore"]]
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@
rawMinQualityScore <<- trimmingPos[["rawMinQualityScore"]]
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@
trimmedStartPos <<- trimmingPos[["trimmedStartPos"]]
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@
trimmedFinishPos <<- trimmingPos[["trimmedFinishPos"]]
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@
trimmedSeqLength <<- trimmingPos[["trimmedSeqLength"]]
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@
trimmedMeanQualityScore <<- trimmingPos[["trimmedMeanQualityScore"]]
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@
trimmedMinQualityScore <<- trimmingPos[["trimmedMinQualityScore"]]
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@
remainingRatio <<- trimmingPos[["remainingRatio"]]
trimmedRV[["rawSeqLength"]] <<-
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@rawSeqLength
trimmedRV[["rawMeanQualityScore"]] <<-
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@
rawMeanQualityScore
trimmedRV[["rawMinQualityScore"]] <<-
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@rawMinQualityScore
trimmedRV[["trimmedStartPos"]] <<-
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@trimmedStartPos
trimmedRV[["trimmedFinishPos"]] <<-
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@trimmedFinishPos
trimmedRV[["trimmedSeqLength"]] <<-
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@trimmedSeqLength
trimmedRV[["trimmedMeanQualityScore"]] <<-
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@
trimmedMeanQualityScore
trimmedRV[["trimmedMinQualityScore"]] <<-
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@
trimmedMinQualityScore
trimmedRV[["remainingRatio"]] <<-
round(SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@
remainingRatio * 100, 2)
} else if (directionParam == "Reverse") {
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@
rawSeqLength <<- trimmingPos[["rawSeqLength"]]
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@
rawMeanQualityScore <<- trimmingPos[["rawMeanQualityScore"]]
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@
rawMinQualityScore <<- trimmingPos[["rawMinQualityScore"]]
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@
trimmedStartPos <<- trimmingPos[["trimmedStartPos"]]
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@
trimmedFinishPos <<- trimmingPos[["trimmedFinishPos"]]
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@
trimmedSeqLength <<- trimmingPos[["trimmedSeqLength"]]
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@
trimmedMeanQualityScore <<- trimmingPos[["trimmedMeanQualityScore"]]
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@
trimmedMinQualityScore <<- trimmingPos[["trimmedMinQualityScore"]]
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@
remainingRatio <<- trimmingPos[["remainingRatio"]]
trimmedRV[["rawSeqLength"]] <<-
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@rawSeqLength
trimmedRV[["rawMeanQualityScore"]] <<-
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@
rawMeanQualityScore
trimmedRV[["rawMinQualityScore"]] <<-
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@rawMinQualityScore
trimmedRV[["trimmedStartPos"]] <<-
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@trimmedStartPos
trimmedRV[["trimmedFinishPos"]] <<-
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@trimmedFinishPos
trimmedRV[["trimmedSeqLength"]] <<-
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@trimmedSeqLength
trimmedRV[["trimmedMeanQualityScore"]] <<-
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@
trimmedMeanQualityScore
trimmedRV[["trimmedMinQualityScore"]] <<-
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@
trimmedMinQualityScore
trimmedRV[["remainingRatio"]] <<-
round(SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@
remainingRatio * 100, 2)
}
}
})
### ------------------------------------------------------------------------
### observeEvent: Button chromatogram parameters re-calculating UI
### ------------------------------------------------------------------------
observeEvent(input$saveChromatogramParam, {
sidebar_menu <- tstrsplit(input$sidebar_menu, " ")
contigIndex <- strtoi(sidebar_menu[[1]])
readIndex <- strtoi(sidebar_menu[[4]])
directionParam <- sidebar_menu[[5]]
### ------------------------------------------------------------
### Update ChromatogramBasePerRow
### ------------------------------------------------------------
if (!is.na(contigIndex) &&
!is.na(readIndex)) {
if (directionParam == "Forward") {
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@ChromatogramParam@
baseNumPerRow <<- input$ChromatogramBasePerRow
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@ChromatogramParam@
heightPerRow <<- input$ChromatogramHeightPerRow
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@ChromatogramParam@
signalRatioCutoff <<- input$ChromatogramSignalRatioCutoff
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@ChromatogramParam@
showTrimmed <<- input$ChromatogramCheckShowTrimmed
} else if (directionParam == "Reverse") {
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@ChromatogramParam@
baseNumPerRow <<- input$ChromatogramBasePerRow
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@ChromatogramParam@
heightPerRow <<- input$ChromatogramHeightPerRow
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@ChromatogramParam@
signalRatioCutoff <<- input$ChromatogramSignalRatioCutoff
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@ChromatogramParam@
showTrimmed <<- input$ChromatogramCheckShowTrimmed
}
### ----------------------------------------------------------------
### Save 'ChromatogramParam' dynamic value
### ----------------------------------------------------------------
ChromatogramParam[["baseNumPerRow"]] <<-
input$ChromatogramBasePerRow
ChromatogramParam[["heightPerRow"]] <<-
input$ChromatogramHeightPerRow
ChromatogramParam[["signalRatioCutoff"]] <<-
input$ChromatogramSignalRatioCutoff
ChromatogramParam[["showTrimmed"]] <<-
input$ChromatogramCheckShowTrimmed
}
})
############################################################################
### SangerAlignment
############################################################################
### ------------------------------------------------------------------------
### Alignment
### ------------------------------------------------------------------------
output$sangerAlignmentAlignmentHTML<-renderUI({
if (input$sidebar_menu == "Contigs Alignment Overview Page _") {
browseSeqHTML <-
file.path(shinyDirectory,
"_SangerAlignment_BrowseSeqs.html")
if (!identical(sangerAlignmentParam[["contigsAlignment"]], character(0))) {
BrowseSeqs(DNAStringSet(sangerAlignmentParam[["contigsAlignment"]]) ,
openURL=FALSE, htmlFile=browseSeqHTML)
}
log_info("file.exists(browseSeqHTML): ", file.exists(browseSeqHTML))
log_info("(browseSeqHTML): ", (browseSeqHTML))
if (file.exists(browseSeqHTML)) {
column(width = 12,
includeHTML(browseSeqHTML),
style = paste("height:100%; ",
"overflow-y: hidden;",
"overflow-x: scroll;")
)
} else {
h4("*** The number of contigs is less than 2.
sCannot create 'BrowseSeqs' alignment. ***",
style="font-weight: bold; font-style: italic;")
}
}
})
### ------------------------------------------------------------------------
### Contigs Tree
### ------------------------------------------------------------------------
output$SATreePlotUI <- renderUI({
if (input$sidebar_menu == "Contigs Alignment Overview Page _") {
if (sangerAlignmentParam[["contigsTree"]]$tip.label != '' &&
!is.null(sangerAlignmentParam[["contigsTree"]]$tip.label)) {
plotOutput("SATreePlot")
} else {
h4("*** The number of contigs is less than 3 or quality of reads are too low.
'Contigs Tree' cannot be created. ***",
style="font-weight: bold; font-style: italic;")
}
}
})
output$SATreePlot <- renderPlot({
if (input$sidebar_menu == "Contigs Alignment Overview Page _") {
plot(sangerAlignmentParam[["contigsTree"]])
}
})
############################################################################
### SangerContig / SangerAlignment Share
############################################################################
### ------------------------------------------------------------------------
### genetic code
### ------------------------------------------------------------------------
output$geneticCodeDF <- renderExcel({
SAGeneticCode <- SangerAlignment@geneticCode
suppressMessages(
excelTable(data = t(data.frame(SAGeneticCode)),
defaultColWidth = 50, editable = FALSE, rowResize = FALSE,
columnResize = FALSE, allowInsertRow = FALSE,
allowInsertColumn = FALSE, allowDeleteRow = FALSE,
allowDeleteColumn = FALSE, allowRenameColumn = FALSE)
)
})
### ------------------------------------------------------------------------
### refAminoAcidSeq
### ------------------------------------------------------------------------
output$SArefAminoAcidSeq <- renderUI({
if (SangerAlignment@refAminoAcidSeq == "") {
box(title = tags$p("Reference Amino Acid Sequence",
style = "font-size: 24px;
font-weight: bold;"),
collapsible = TRUE,
status = "success", width = 12,
column(width = 1),
column(width = 11,
h4("Reference Amino Acid Sequence is not provided."))
)
} else {
box(title = tags$p("Reference Amino Acid Sequence",
style = "font-size: 24px;
font-weight: bold;"),
collapsible = TRUE,
status = "success", width = 12,
column(width = 2,
tags$br(),
tags$p("AA Sequence:",
style = "font-size: 15px;
font-weight: bold;"),
),
column(width = 10,
excelOutput("SArefAminoAcidSeqDF",
width = "100%", height = "50"),
style = paste("height:100%; ",
"overflow-y: hidden;",
"overflow-x: scroll;")
),
)
}
})
output$SArefAminoAcidSeqDF <- renderExcel({
refAminoAcidSeqVec <-
strsplit(SangerAlignment@refAminoAcidSeq, "")[[1]]
names(refAminoAcidSeqVec) <- c(seq_len(length(refAminoAcidSeqVec)))
suppressMessages(
excelTable(data =
t(data.frame(refAminoAcidSeqVec)),
defaultColWidth = 50, editable = FALSE, rowResize = FALSE,
columnResize = FALSE, allowInsertRow = FALSE,
allowInsertColumn = FALSE, allowDeleteRow = FALSE,
allowDeleteColumn = FALSE, allowRenameColumn = FALSE)
)
})
############################################################################
### SangerContig
############################################################################
valueBoxSAMinReadsNum (input, output, SangerAlignment, session)
valueBoxSAMinReadLength (input, output, SangerAlignment, session)
valueBoxSAMinFractionCall (input, output, SangerAlignment, session)
valueBoxSAMaxFractionLost (input, output, SangerAlignment, session)
valueBoxSAAcceptStopCodons (input, output, SangerAlignment, session)
valueBoxSAReadingFrame (input, output, SangerAlignment, session)
### ------------------------------------------------------------------------
### Alignment
### ------------------------------------------------------------------------
output$contigAlignmentHTML<-renderUI({
sidebar_menu <- tstrsplit(input$sidebar_menu, " ")
contigIndex <- strtoi(sidebar_menu[[1]])
if (!is.na(contigIndex)) {
browseSeqHTML <-
file.path(shinyDirectory, "BrowseSeqs_html",
paste0(sidebar_menu[[1]], "_",
contigParam[["contigName"]],
"_Alignment_BrowseSeqs.html"))
if (!dir.exists(file.path(shinyDirectory, "BrowseSeqs_html"))) {
dir.create(file.path(shinyDirectory, "BrowseSeqs_html"))
}
BrowseSeqs(DNAStringSet(contigParam[["alignment"]]),
openURL=FALSE, htmlFile=browseSeqHTML)
column(width = 12,
includeHTML(browseSeqHTML),
style = paste("height:100%; ",
"overflow-y: hidden;",
"overflow-x: scroll;")
)
}
})
### ------------------------------------------------------------------------
### difference
### ------------------------------------------------------------------------
output$SADifferencesDFUI <- renderUI({
sidebar_menu <- tstrsplit(input$sidebar_menu, " ")
contigIndex <- strtoi(sidebar_menu[[1]])
if (!is.na(contigIndex)) {
if (all(dim(contigParam[["differencesDF"]]) == c(0,0))) {
h4("*** 'Differences' dataframe is empty. ***",
style="font-weight: bold; font-style: italic;")
} else {
dataTableOutput("SADifferencesDF")
}
}
})
output$SADifferencesDF = renderDataTable({
contigParam[["differencesDF"]]
})
### ------------------------------------------------------------------------
### dendrogram
### ------------------------------------------------------------------------
output$dendrogramPlot <- renderPlot({
sidebar_menu <- tstrsplit(input$sidebar_menu, " ")
contigIndex <- strtoi(sidebar_menu[[1]])
if (!is.na(contigIndex)) {
ggdendrogram(contigParam[["dendrogram"]][[2]], rotate = TRUE)
}
})
output$dendrogramDF <- renderDataTable({
sidebar_menu <- tstrsplit(input$sidebar_menu, " ")
contigIndex <- strtoi(sidebar_menu[[1]])
if (!is.na(contigIndex)) {
contigParam[["dendrogram"]][[1]]
}
})
### ------------------------------------------------------------------------
### distance
### ------------------------------------------------------------------------
output$SADistanceMatrixPlotUI <- renderUI({
sidebar_menu <- tstrsplit(input$sidebar_menu, " ")
contigIndex <- strtoi(sidebar_menu[[1]])
if (!is.na(contigIndex)) {
if (all(dim(contigParam[["distanceMatrix"]]) == c(0,0))) {
h4("*** 'Distance' dataframe is empty. (Cannot plot)***",
style="font-weight: bold; font-style: italic;")
} else {
plotlyOutput("SADistanceMatrixPlot")
}
}
})
output$SADistanceMatrixPlot <- renderPlotly({
sidebar_menu <- tstrsplit(input$sidebar_menu, " ")
contigIndex <- strtoi(sidebar_menu[[1]])
if (!is.na(contigIndex)) {
SangerReadBFN <-
SangerAlignmentParam[[contigIndex]]$SangerReadBFN
suppressPlotlyMessage(
plot_ly(x = SangerReadBFN,
y = SangerReadBFN,
z = contigParam[["distanceMatrix"]],
colors = colorRamp(c("white", "#32a852")),
type = "heatmap")
)
}
})
output$SADistanceMatrixUI <- renderUI({
sidebar_menu <- tstrsplit(input$sidebar_menu, " ")
contigIndex <- strtoi(sidebar_menu[[1]])
if (!is.na(contigIndex)) {
if (all(dim(contigParam[["distanceMatrix"]]) == c(0,0))) {
h4("*** 'Distance' dataframe is empty. ***",
style="font-weight: bold; font-style: italic;")
} else {
dataTableOutput("SADistanceMatrix")
}
}
})
output$SADistanceMatrix = renderDataTable({
contigParam[["distanceMatrix"]]
})
### ------------------------------------------------------------------------
### SAIndelsDF
### ------------------------------------------------------------------------
output$SAIndelsDFUI <- renderUI({
sidebar_menu <- tstrsplit(input$sidebar_menu, " ")
contigIndex <- strtoi(sidebar_menu[[1]])
if (!is.na(contigIndex)) {
if (all(dim(contigParam[["indelsDF"]] ) == c(0,0))) {
h4("*** 'Indels' data frame is empty. ***",
style="font-weight: bold; font-style: italic;")
} else {
dataTableOutput("SAIndelsDF")
}
}
})
output$SAIndelsDF <- renderDataTable({
contigParam[["indelsDF"]]
})
### ------------------------------------------------------------------------
### SAStopCodons
### ------------------------------------------------------------------------
output$SAStopCodonsDFUI <- renderUI({
sidebar_menu <- tstrsplit(input$sidebar_menu, " ")
contigIndex <- strtoi(sidebar_menu[[1]])
if (!is.na(contigIndex)) {
if (all(dim(contigParam[["stopCodonsDF"]]) == c(0,0))) {
h4("*** 'Stop Codons' dataframe is empty. ***",
style="font-weight: bold; font-style: italic;")
} else {
dataTableOutput("SAStopCodonsDF")
}
}
})
output$SAStopCodonsDF <- renderDataTable({
contigParam[["stopCodonsDF"]]
})
############################################################################
### SangerRead (Function for singel read in contigSeq)
############################################################################
output$primarySeqDF <- renderExcel({
sidebar_menu <- tstrsplit(input$sidebar_menu, " ")
contigIndex <- strtoi(sidebar_menu[[1]])
readIndex <- strtoi(sidebar_menu[[4]])
directionParam <- sidebar_menu[[5]]
if (!is.na(contigIndex) &&
!is.na(readIndex)) {
primarySeqDisplay (sequenceParam, colors=colors)
}
})
output$secondSeqDF <- renderExcel({
sidebar_menu <- tstrsplit(input$sidebar_menu, " ")
contigIndex <- strtoi(sidebar_menu[[1]])
readIndex <- strtoi(sidebar_menu[[4]])
directionParam <- sidebar_menu[[5]]
if (!is.na(contigIndex) &&
!is.na(readIndex)) {
secondarySeqDisplay (sequenceParam, colors=colors)
}
})
output$qualityScoreDF <- renderExcel({
sidebar_menu <- tstrsplit(input$sidebar_menu, " ")
contigIndex <- strtoi(sidebar_menu[[1]])
readIndex <- strtoi(sidebar_menu[[4]])
directionParam <- sidebar_menu[[5]]
if (!is.na(contigIndex) &&
!is.na(readIndex)) {
if (directionParam == "Forward") {
PhredScore <-
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@
QualityReport@qualityPhredScores
} else if (directionParam == "Reverse") {
PhredScore <-
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@
QualityReport@qualityPhredScores
}
qualityScoreDisplay (PhredScore)
}
})
output$PrimAASeqS1DF <- renderExcel({
sidebar_menu <- tstrsplit(input$sidebar_menu, " ")
contigIndex <- strtoi(sidebar_menu[[1]])
readIndex <- strtoi(sidebar_menu[[4]])
directionParam <- sidebar_menu[[5]]
if (!is.na(contigIndex) &&
!is.na(readIndex)) {
PrimAASeqS1Display (sequenceParam)
}
})
output$PrimAASeqS2DF <- renderExcel({
sidebar_menu <- tstrsplit(input$sidebar_menu, " ")
contigIndex <- strtoi(sidebar_menu[[1]])
readIndex <- strtoi(sidebar_menu[[4]])
directionParam <- sidebar_menu[[5]]
if (!is.na(contigIndex) &&
!is.na(readIndex)) {
PrimAASeqS2Display (sequenceParam)
}
})
output$PrimAASeqS3DF <- renderExcel({
sidebar_menu <- tstrsplit(input$sidebar_menu, " ")
contigIndex <- strtoi(sidebar_menu[[1]])
readIndex <- strtoi(sidebar_menu[[4]])
directionParam <- sidebar_menu[[5]]
if (!is.na(contigIndex) &&
!is.na(readIndex)) {
PrimAASeqS3Display (sequenceParam)
}
})
output$primarySeqTrimmedDF <- renderExcel({
sidebar_menu <- tstrsplit(input$sidebar_menu, " ")
contigIndex <- strtoi(sidebar_menu[[1]])
readIndex <- strtoi(sidebar_menu[[4]])
directionParam <- sidebar_menu[[5]]
if (!is.na(contigIndex) &&
!is.na(readIndex)) {
primarySeqTrimmedDisplay (input, output, session,
sequenceParam, trimmedRV, colors=colors)
}
})
output$secondSeqTrimmedDF <- renderExcel({
sidebar_menu <- tstrsplit(input$sidebar_menu, " ")
contigIndex <- strtoi(sidebar_menu[[1]])
readIndex <- strtoi(sidebar_menu[[4]])
directionParam <- sidebar_menu[[5]]
if (!is.na(contigIndex) &&
!is.na(readIndex)) {
secondSeqTrimmedDisplay (input, output, session,
sequenceParam, trimmedRV, colors=colors)
}
})
output$qualityScoreTrimmedDF <- renderExcel({
sidebar_menu <- tstrsplit(input$sidebar_menu, " ")
contigIndex <- strtoi(sidebar_menu[[1]])
readIndex <- strtoi(sidebar_menu[[4]])
directionParam <- sidebar_menu[[5]]
if (!is.na(contigIndex) &&
!is.na(readIndex)) {
if (directionParam == "Forward") {
PhredScore <-
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@
QualityReport@qualityPhredScores[
(trimmedRV[["trimmedStartPos"]]+1):
trimmedRV[["trimmedFinishPos"]]]
} else if (directionParam == "Reverse") {
PhredScore <-
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@
QualityReport@qualityPhredScores[
(trimmedRV[["trimmedStartPos"]]+1):
trimmedRV[["trimmedFinishPos"]]]
}
qualityScoreDisplay (PhredScore)
}
})
############################################################################
### Trimming method selection functions
############################################################################
### ------------------------------------------------------------------------
### Trimming Method Selection (Just check forward reads => not dynamic)
### ------------------------------------------------------------------------
output$TrimmingMethodSelectionOutput <- renderUI({
sidebar_menu <- tstrsplit(input$sidebar_menu, " ")
contigIndex <- strtoi(sidebar_menu[[1]])
readIndex <- strtoi(sidebar_menu[[4]])
if (!is.na(contigIndex) &&
!is.na(readIndex)) {
if (SangerAlignment@contigList[[contigIndex]]@forwardReadList[[readIndex]]@QualityReport@TrimmingMethod == "M1") {
tagList(icon("check-circle"),
"Your trimming method selection :
'Modified Mott Trimming'")
} else if (SangerAlignment@contigList[[contigIndex]]@forwardReadList[[readIndex]]@QualityReport@TrimmingMethod == "M2") {
tagList(icon("check-circle"),
"Your trimming method selection :
'Trimmomatics Sliding Window Trimming'")
}
}
})
output$TrimmingMethodUI <- renderUI({
sidebar_menu <- tstrsplit(input$sidebar_menu, " ")
contigIndex <- strtoi(sidebar_menu[[1]])
readIndex <- strtoi(sidebar_menu[[4]])
directionParam <- sidebar_menu[[5]]
if (!is.na(contigIndex) &&
!is.na(readIndex)) {
if (directionParam == "Forward") {
activated_read_list <- SangerAlignment@contigList[[contigIndex]]@forwardReadList
} else if (directionParam == "Reverse") {
activated_read_list <- SangerAlignment@contigList[[contigIndex]]@reverseReadList
}
if (activated_read_list[[readIndex]]@QualityReport@TrimmingMethod == "M1") {
if (directionParam == "Forward") {
if (is.null(SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@
QualityReport@M1TrimmingCutoff)) {
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@
QualityReport@M1TrimmingCutoff <<- 0.0001
}
} else if (directionParam == "Reverse") {
if (is.null(SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@
QualityReport@M1TrimmingCutoff)) {
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@
QualityReport@M1TrimmingCutoff <<- 0.0001
}
}
fluidRow(
column(6,
uiOutput("M1TrimmingCutoff") ,
tags$ul(
textInput("M1TrimmingCutoffText",
label = p("Change Value"),
value = toString(
trimmedParam[["M1TrimmingCutoff"]]),
width = '70%')
),
),
)
} else if (activated_read_list[[readIndex]]@QualityReport@TrimmingMethod == "M2") {
if (directionParam == "Forward") {
if (is.null(SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@
QualityReport@M2CutoffQualityScore)) {
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@
QualityReport@M2CutoffQualityScore <<- 20
}
if (is.null(SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@
QualityReport@M2SlidingWindowSize )) {
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@
QualityReport@M2SlidingWindowSize <<- 10
}
} else if (directionParam == "Reverse") {
if (is.null(SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@
QualityReport@M2CutoffQualityScore)) {
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@
QualityReport@M2CutoffQualityScore <<- 20
}
if (is.null(SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@
QualityReport@M2SlidingWindowSize )) {
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@
QualityReport@M2SlidingWindowSize <<- 10
}
}
fluidRow(
column(6,
uiOutput("M2CutoffQualityScore") ,
tags$ul(
textInput("M2CutoffQualityScoreText",
label = p("Change Value"),
value = toString(
trimmedParam[["M2CutoffQualityScore"]]),
width = '70%')
),
),
column(6,
uiOutput("M2SlidingWindowSize") ,
tags$ul(
textInput("M2SlidingWindowSizeText",
label = p("Change Value"),
value = toString(
trimmedParam[["M2SlidingWindowSize"]]),
width = '70%')
),
),
)
}
}
})
valueBoxM1TrimmingCutoff (input, output, session)
valueBoxM2CutoffQualityScore (input, output, session)
valueBoxM2SlidingWindowSize (input, output, session)
valueBoxRawSeqLength (input, output, session, trimmedRV)
valueBoxRawMeanQualityScore (input, output, session, trimmedRV)
valueBoxRawMinQualityScore (input, output, session, trimmedRV)
valueBoxTrimmedStartPos (input, output, session, trimmedRV)
valueBoxTrimmedFinishPos (input, output, session, trimmedRV)
valueBoxTrimmedSeqLength (input, output, session, trimmedRV)
valueBoxTrimmedMeanQualityScore (input, output, session, trimmedRV)
valueBoxTrimmedMinQualityScore (input, output, session, trimmedRV)
valueBoxRemainingRatio (input, output, session, trimmedRV)
output$qualityQualityBasePlot <- renderPlotly({
sidebar_menu <- tstrsplit(input$sidebar_menu, " ")
contigIndex <- strtoi(sidebar_menu[[1]])
readIndex <- strtoi(sidebar_menu[[4]])
directionParam <- sidebar_menu[[5]]
if (!is.na(contigIndex) &&
!is.na(readIndex)) {
if (directionParam == "Forward") {
qualityPhredScores <-
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@
QualityReport@qualityPhredScores
} else if (directionParam == "Reverse") {
qualityPhredScores <-
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@
QualityReport@qualityPhredScores
}
qualityQualityBasePlotDisplay(input, output,session,
trimmedRV, qualityPhredScores)
}
})
valueBoxChromTrimmedStartPos (input, output, session, trimmedRV)
valueBoxChromTrimmedFinishPos (input, output, session, trimmedRV)
# chromatogram
output$chromatogramUIOutput <- renderUI({
sidebar_menu <- tstrsplit(input$sidebar_menu, " ")
contigIndex <- strtoi(sidebar_menu[[1]])
readIndex <- strtoi(sidebar_menu[[4]])
directionParam <- sidebar_menu[[5]]
if (sidebar_menu[[2]] == "Contig" &&
sidebar_menu[[3]] == "-" &&
!is.na(readIndex) &&
(directionParam == "Forward" ||
directionParam == "Reverse") &&
sidebar_menu[[6]] == "Read") {
trimmedRV[["trimmedSeqLength"]]
if (directionParam == "Forward") {
rawSeqLength <-
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@
QualityReport@rawSeqLength
trimmedSeqLength <-
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@
QualityReport@trimmedSeqLength
} else if (directionParam == "Reverse") {
rawSeqLength <-
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@
QualityReport@rawSeqLength
trimmedSeqLength <-
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@
QualityReport@trimmedSeqLength
}
chromatogramRowNumAns <- chromatogramRowNum (
strtoi(ChromatogramParam[["baseNumPerRow"]]),
rawSeqLength, trimmedSeqLength,
ChromatogramParam[["showTrimmed"]]) *
strtoi(ChromatogramParam[["heightPerRow"]])
plotOutput("chromatogram", height = chromatogramRowNumAns)
}
})
output$chromatogram <- renderPlot({
## !!!!! Update !!!!
shinyjs::disable("startTrimmingButton")
shinyjs::disable("saveChromatogramParam")
shinyjs::disable("ChromatogramBasePerRow")
shinyjs::disable("ChromatogramHeightPerRow")
shinyjs::disable("ChromatogramSignalRatioCutoff")
shinyjs::disable("ChromatogramCheckShowTrimmed")
shinyjs::disable("M1TrimmingCutoffText")
shinyjs::disable("M2CutoffQualityScoreText")
shinyjs::disable("M2SlidingWindowSizeText")
sidebar_menu <- tstrsplit(input$sidebar_menu, " ")
contigIndex <- strtoi(sidebar_menu[[1]])
readIndex <- strtoi(sidebar_menu[[4]])
directionParam <- sidebar_menu[[5]]
if (sidebar_menu[[2]] == "Contig" &&
sidebar_menu[[3]] == "-" &&
!is.na(readIndex) &&
(directionParam == "Forward" ||
directionParam == "Reverse") &&
sidebar_menu[[6]] == "Read") {
removeNotification(id = "saveNotification")
showNotification(
ui = fluidRow(
column(1),
column(11,
tags$p(tagList(icon("hourglass-start"),
"Plotting Chromatogram ... "),
style = "font-size: 28px;
font-weight: bold;"),
tags$p(tagList(icon("dot-circle"),
"Base pairs per row : ",
ChromatogramParam[["baseNumPerRow"]]),
style = "font-size: 20px;
font-style: italic"),
tags$p(tagList(icon("dot-circle"),
"Height per row : ",
ChromatogramParam[["heightPerRow"]]),
style = "font-size: 20px;
font-style: italic"),
tags$p(tagList(icon("dot-circle"),
"Signal Ratio Cutoff : ",
ChromatogramParam[["signalRatioCutoff"]]),
style = "font-size: 20px;
font-style: italic"),
tags$p(tagList(icon("dot-circle"),
"Show trimmed : ",
ChromatogramParam[["showTrimmed"]]),
style = "font-size: 20px;
font-style: italic"),
tags$p("( If 'Signal Ratio Cutoff' is too small,
it would need more time to replot
the chromatogram)",
style = "font-size: 16px;
font-style: italic"),)
),
action = NULL, duration = NULL, closeButton = FALSE,
id = "chromatogramNotification",
type = "message")
if (directionParam == "Forward") {
rawSeqLength <-
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@rawSeqLength
log_info(">>>>>>>>>>>> Re-running 'MakeBaseCalls' function (forward)")
### ----------------------------------------------------------------
### Re-run 'MakeBaseCall' function
### ----------------------------------------------------------------
hetcalls <-
MakeBaseCalls(SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]],
signalRatioCutoff = as.numeric(
ChromatogramParam[["signalRatioCutoff"]]))
### ----------------------------------------------------------------
### Update 'SangerContig'!
### ----------------------------------------------------------------
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@peakPosMatrix <<-
hetcalls@peakPosMatrix
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@peakAmpMatrix <<-
hetcalls@peakAmpMatrix
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@primarySeq <<-
hetcalls@primarySeq
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@secondarySeq <<-
hetcalls@secondarySeq
### ----------------------------------------------------------------
### Updating AASeqs
### ----------------------------------------------------------------
AASeqResult <- calculateAASeq (hetcalls@primarySeq,
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@trimmedStartPos,
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@trimmedFinishPos,
SangerAlignment@geneticCode)
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@primaryAASeqS1 <<-
AASeqResult[["primaryAASeqS1"]]
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@primaryAASeqS2 <<-
AASeqResult[["primaryAASeqS2"]]
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@primaryAASeqS3 <<-
AASeqResult[["primaryAASeqS3"]]
### ----------------------------------------------------------------
### Updating reactive values
### ----------------------------------------------------------------
sequenceParam[["primarySeq"]] <<-
as.character(SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@primarySeq)
sequenceParam[["secondarySeq"]] <<-
as.character(SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@secondarySeq)
sequenceParam[["primaryAASeqS1"]] <<-
as.character(SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@primaryAASeqS1)
sequenceParam[["primaryAASeqS2"]] <<-
as.character(SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@primaryAASeqS2)
sequenceParam[["primaryAASeqS3"]] <<-
as.character(SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@primaryAASeqS3)
} else if (directionParam == "Reverse") {
rawSeqLength <-
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@rawSeqLength
log_info(">>>>>>>>>>>> Re-running 'MakeBaseCalls' function (reverse)")
### ----------------------------------------------------------------
### Re-run 'MakeBaseCall' function
### ----------------------------------------------------------------
hetcalls <-
MakeBaseCalls(SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]],
signalRatioCutoff = as.numeric(
ChromatogramParam[["signalRatioCutoff"]]))
### ------------------------------------------------------------
### Update 'SangerContig'!
### ------------------------------------------------------------
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@peakPosMatrix <<-
hetcalls@peakPosMatrix
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@peakAmpMatrix <<-
hetcalls@peakAmpMatrix
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@primarySeq <<-
hetcalls@primarySeq
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@secondarySeq <<-
hetcalls@secondarySeq
### ------------------------------------------------------------
### Updating AASeqs
### ------------------------------------------------------------
AASeqResult <- calculateAASeq (hetcalls@primarySeq,
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@trimmedStartPos,
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@trimmedFinishPos,
SangerAlignment@geneticCode)
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@primaryAASeqS1 <<-
AASeqResult[["primaryAASeqS1"]]
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@primaryAASeqS2 <<-
AASeqResult[["primaryAASeqS2"]]
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@primaryAASeqS3 <<-
AASeqResult[["primaryAASeqS3"]]
### ------------------------------------------------------------
### Updating reactive values
### ------------------------------------------------------------
sequenceParam[["primarySeq"]] <<-
as.character(SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@primarySeq)
sequenceParam[["secondarySeq"]] <<-
as.character(SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@secondarySeq)
sequenceParam[["primaryAASeqS1"]] <<-
as.character(SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@primaryAASeqS1)
sequenceParam[["primaryAASeqS2"]] <<-
as.character(SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@primaryAASeqS2)
sequenceParam[["primaryAASeqS3"]] <<-
as.character(SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@primaryAASeqS3)
}
# log_info(">>>>>>>>>>>> 'MakeBaseCalls' finished")
chromatogram_overwrite(hetcalls,
width = strtoi(
ChromatogramParam[["baseNumPerRow"]]),
height = 2,
trim5 = trimmedRV[["trimmedStartPos"]],
trim3 = rawSeqLength -
trimmedRV[["trimmedFinishPos"]],
showtrim = (ChromatogramParam[["showTrimmed"]]),
showcalls = "both", colors = colors)
removeNotification(id = "chromatogramNotification")
shinyjs::enable("ChromatogramBasePerRow")
shinyjs::enable("ChromatogramHeightPerRow")
shinyjs::enable("ChromatogramSignalRatioCutoff")
shinyjs::enable("ChromatogramCheckShowTrimmed")
shinyjs::enable("M1TrimmingCutoffText")
shinyjs::enable("M2CutoffQualityScoreText")
shinyjs::enable("M2SlidingWindowSizeText")
shinyjs::enable("startTrimmingButton")
shinyjs::enable("saveChromatogramParam")
}
})
}
roblanf/sangeranalyseR documentation built on April 15, 2024, 12:44 a.m.
R Package Documentation
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Defines functions SangerAlignmentServer
### ============================================================================
### R shiny SangerAlignment server function
### ============================================================================
SangerAlignmentServer <- function(input, output, session) {
# Suppress Warning
options(warn = -1)
### ------------------------------------------------------------------------
### SangerAlignment parameters initialization.
### ------------------------------------------------------------------------
SangerAlignment <- getShinyOption("sangerAlignment")
shinyDirectory <- getShinyOption("shinyDirectory")
colors <- getShinyOption("colors")
SangerAlignment <- SangerAlignment[[1]]
SangerAlignmentNum <- length(SangerAlignment@contigList)
SangerAlignmentParam <- lapply(seq_len(SangerAlignmentNum), function(i) {
### --------------------------------------------------------------------
### SangerContig-related parameters initialization.
### --------------------------------------------------------------------
# readFeature
SCName <- paste0(i, " Contig")
# Forward & reverse reads list
SangerReadFReadList <-
SangerAlignment@contigList[[i]]@forwardReadList
SangerReadRReadsList <-
SangerAlignment@contigList[[i]]@reverseReadList
forwardReadNum <- length(SangerReadFReadList)
reverseReadNum <- length(SangerReadRReadsList)
# readFeature
forwardReadFeature <- vapply(seq_len(forwardReadNum), function(j)
paste0(j, " ",
SangerReadFReadList[[j]]@readFeature), character(1))
reverseReadFeature <- vapply(seq_len(reverseReadNum), function(j)
paste0(j, " ",
SangerReadRReadsList[[j]]@readFeature), character(1))
SangerReadFeature <- c(forwardReadFeature, reverseReadFeature)
# readFileName (basename)
forwardReadBFN <- vapply(seq_len(forwardReadNum), function(j)
basename(SangerReadFReadList[[j]]@readFileName), character(1))
reverseReadBFN <- vapply(seq_len(reverseReadNum), function(j)
basename(SangerReadRReadsList[[j]]@readFileName), character(1))
SangerReadBFN <- c(forwardReadBFN, reverseReadBFN)
return(list(SCName = SCName,
forwardReadNum = forwardReadNum,
reverseReadNum = reverseReadNum,
forwardReadFeature = forwardReadFeature,
reverseReadFeature = reverseReadFeature,
SangerReadBFN = SangerReadBFN))
})
### ------------------------------------------------------------------------
### SangerAlignment reactiveValue
### ------------------------------------------------------------------------
sangerAlignmentParam <-
reactiveValues(
contigsConsensus = SangerAlignment@contigsConsensus,
contigsAlignment = as.character(SangerAlignment@contigsAlignment),
contigsTree = SangerAlignment@contigsTree)
### ------------------------------------------------------------------------
### SangerContig reactiveValue
### ------------------------------------------------------------------------
contigParam <-
reactiveValues(
contigName = NULL,
contigSeq = NULL,
differencesDF = NULL,
alignment = NULL,
distanceMatrix = NULL,
dendrogram = NULL,
indelsDF = NULL,
stopCodonsDF = NULL,
secondaryPeakDF = NULL)
### ------------------------------------------------------------------------
### SingleRead reactiveValue
### ------------------------------------------------------------------------
sequenceParam <- reactiveValues(primarySeq = "",
secondarySeq = "",
primaryAASeqS1 = "",
primaryAASeqS2 = "",
primaryAASeqS3 = "")
trimmedRV <- reactiveValues(rawSeqLength = 0,
rawMeanQualityScore = 0,
rawMinQualityScore = 0,
trimmedStartPos = 0,
trimmedFinishPos = 0,
trimmedSeqLength = 0,
trimmedMeanQualityScore = 0,
trimmedMinQualityScore = 0,
remainingRatio = 0)
trimmedParam <- reactiveValues(M1TrimmingCutoff = 0,
M2CutoffQualityScore = 0,
M2SlidingWindowSize = 0)
ChromatogramParam <- reactiveValues(baseNumPerRow = 0,
heightPerRow = 0,
signalRatioCutoff = 0,
showTrimmed = TRUE)
############################################################################
### Main panel dynamic UI
############################################################################
output$aligned_contigSeq_content <- renderUI({
sidebar_menu <- tstrsplit(input$sidebar_menu, " ")
if (sidebar_menu[[1]] == "Contigs" &&
sidebar_menu[[2]] == "Alignment" &&
sidebar_menu[[3]] == "Overview" &&
sidebar_menu[[4]] == "Page" &&
sidebar_menu[[5]] == "_" ) {
h1(input$sidebar_menu)
log_info(">>>>>>>> Inside 'Contigs Alignment Overview Page _'")
shinyjs::disable("closeUI")
shinyjs::disable("recalculateButtonSA")
log_info("######## Reactive button clicked !!!")
log_info("######## Start re-aligning contigs")
CSSetResult <-
alignContigs (SangerAlignment@contigList,
SangerAlignment@geneticCode,
SangerAlignment@refAminoAcidSeq,
SangerAlignment@contigList[[1]]@minFractionCall,
SangerAlignment@contigList[[1]]@maxFractionLost,
1)
SangerAlignment@contigsConsensus <<- CSSetResult$consensus
SangerAlignment@contigsAlignment <<- CSSetResult$aln
SangerAlignment@contigsTree <<- CSSetResult$aln.tree
sangerAlignmentParam[["contigsConsensus"]] <<- SangerAlignment@contigsConsensus
sangerAlignmentParam[["contigsAlignment"]] <<- as.character(SangerAlignment@contigsAlignment)
sangerAlignmentParam[["contigsTree"]] <<- SangerAlignment@contigsTree
log_info("######## Finish contigs re-alignment")
shinyjs::enable("recalculateButtonSA")
shinyjs::enable("closeUI")
fluidRow(
useShinyjs(),
box(title = tags$p("Input Parameters: ",
style = "font-size: 26px;
font-weight: bold;"),
solidHeader = TRUE, collapsible = TRUE,
status = "success", width = 12,
tags$hr(style = ("border-top: 0.2px hidden #A9A9A9;")),
fluidRow(
column(width = 12,
actionBttn("recalculateButtonSA",
"Re-calculate Contigs Alignment",
icon = icon("calculator"),
style = "simple", color = "danger",
block = TRUE, size = "lg")
),
column(12,
tags$hr(
style = ("border-top: 2px hidden #A9A9A9;"))
),
column(12,
column(3,
tags$p(tagList(icon("caret-right"),
"Output Directory: "),
style = "font-size: 20px;
font-weight: bold;"),
),
column(9,
h4(shinyDirectory),
)
),
column(12,
column(3,
tags$p(
tagList(icon("caret-right"),
"Raw ABI Parent Directory:"),
style = "font-size: 20px;
font-weight: bold;"),
),
column(9,
h4(SangerAlignment@ABIF_Directory),
)
),
column(12,
column(3,
tags$p(tagList(icon("caret-right"),
"Forward Suffix RegExp: "),
style = "font-size: 20px;
font-weight: bold;"),
),
column(9,
h4(SangerAlignment@REGEX_SuffixForward),
)
),
column(12,
column(3,
tags$p(tagList(icon("caret-right"),
"Reverse Suffix RegExp: "),
style = "font-size: 20px;
font-weight: bold;"),
),
column(9,
h4(SangerAlignment@REGEX_SuffixReverse),
)
),
column(12,
column(3,
tags$p(tagList(icon("caret-right"),
"Contigs Number: "),
style = "font-size: 20px;
font-weight: bold;"),
),
column(9,
h4(length(SangerAlignment@
contigList)),
)
),
tags$hr(style = ("border-top: 4px hidden #A9A9A9;")),
box(title = tags$p("Genetic Code Data Frame",
style = "font-size: 24px;
font-weight: bold;"),
collapsible = TRUE,
status = "success", width = 12,
column(width = 2,
tags$p("Tri-nucleotide:",
style = "font-size: 15px;
font-weight: bold;"),
tags$p("Amino Acid : ",
style = "font-size: 15px;
font-weight: bold;"),
tags$p("('*' : stop codon) ",
style = "font-size: 12px;
font-weight: italic;"),
),
column(width = 10,
excelOutput("geneticCodeDF",
width = "100%", height = "50"),
style = paste("height:100%; ",
"overflow-y: hidden;",
"overflow-x: scroll;")
),
),
uiOutput("SArefAminoAcidSeq") ,
),
),
box(title = tags$p(tagList(icon("dot-circle"),
"SangerAlignment Results: "),
style = "font-size: 26px;
font-weight: bold;"),
solidHeader = TRUE, collapsible = TRUE,
status = "success", width = 12,
tags$hr(style = ("border-top: 4px hidden #A9A9A9;")),
box(title = tags$p("Contigs Alignment",
style = "font-size: 24px;
font-weight: bold;"),
collapsible = TRUE,
status = "success", width = 12,
column(width = 12,
htmlOutput("sangerAlignmentAlignmentHTML"),
),
),
box(title = tags$p("Contigs Tree",
style = "font-size: 24px;
font-weight: bold;"),
collapsible = TRUE,
status = "success", width = 12,
column(width = 12,
# uiOutput("SATreePlotUI"),
plotOutput("SATreePlot"),
style = paste("height:100%; overflow-y:",
"scroll;overflow-x: scroll;")
)
),
),
)
} else if (!is.na(strtoi(sidebar_menu[[1]])) &&
sidebar_menu[[2]] == "Sanger" &&
sidebar_menu[[3]] == "Contig" &&
sidebar_menu[[4]] == "Overview" &&
sidebar_menu[[5]] == "Page") {
contigIndex <- strtoi(sidebar_menu[[1]])
log_info(">>>>>>>> Inside '", input$sidebar_menu, "'")
shinyjs::disable("closeUI")
shinyjs::disable("recalculateButton")
log_info("@@@@@@@ 'Reactive button' has been clicked")
log_info("In the main")
log_info("######## Start recalculating contig")
CSResult<-
calculateContigSeq (
SangerAlignment@contigList[[contigIndex]]@inputSource,
SangerAlignment@contigList[[contigIndex]]@forwardReadList,
SangerAlignment@contigList[[contigIndex]]@reverseReadList,
SangerAlignment@contigList[[contigIndex]]@refAminoAcidSeq,
SangerAlignment@contigList[[contigIndex]]@minFractionCall,
SangerAlignment@contigList[[contigIndex]]@maxFractionLost,
SangerAlignment@contigList[[contigIndex]]@geneticCode,
SangerAlignment@contigList[[contigIndex]]@acceptStopCodons,
SangerAlignment@contigList[[contigIndex]]@readingFrame)
SangerAlignment@contigList[[contigIndex]]@contigSeq <<- CSResult$consensusGapfree
SangerAlignment@contigList[[contigIndex]]@differencesDF <<- CSResult$diffsDf
SangerAlignment@contigList[[contigIndex]]@alignment <<- CSResult$aln2
SangerAlignment@contigList[[contigIndex]]@distanceMatrix <<- CSResult$dist
SangerAlignment@contigList[[contigIndex]]@dendrogram <<- CSResult$dend
SangerAlignment@contigList[[contigIndex]]@indelsDF <<- CSResult$indels
SangerAlignment@contigList[[contigIndex]]@stopCodonsDF <<- CSResult$stopsDf
SangerAlignment@contigList[[contigIndex]]@secondaryPeakDF <<- CSResult$spDf
contigParam[["contigName"]] <<- SangerAlignment@contigList[[contigIndex]]@contigName
contigParam[["contigSeq"]] <<- SangerAlignment@contigList[[contigIndex]]@contigSeq
contigParam[["differencesDF"]] <<- SangerAlignment@contigList[[contigIndex]]@differencesDF
contigParam[["alignment"]] <<- as.character(SangerAlignment@contigList[[contigIndex]]@alignment)
contigParam[["distanceMatrix"]] <<-SangerAlignment@contigList[[contigIndex]]@distanceMatrix
contigParam[["dendrogram"]] <<- SangerAlignment@contigList[[contigIndex]]@dendrogram
contigParam[["indelsDF"]] <<- SangerAlignment@contigList[[contigIndex]]@indelsDF
contigParam[["stopCodonsDF"]] <<- SangerAlignment@contigList[[contigIndex]]@stopCodonsDF
contigParam[["secondaryPeakDF"]] <<- SangerAlignment@contigList[[contigIndex]]@secondaryPeakDF
log_info("######## Finish recalculating contig")
shinyjs::enable("recalculateButton")
shinyjs::enable("closeUI")
fluidRow(
useShinyjs(),
box(title = tags$p(tagList(icon("dot-circle"),
"Basic Information: "),
style = "font-size: 26px;
font-weight: bold;"),
solidHeader = TRUE, collapsible = TRUE,
status = "success", width = 12,
tags$hr(
style = ("border-top: 0.2px hidden #A9A9A9;")),
fluidRow(
column(width = 12,
actionBttn("recalculateButton",
"Re-calculate Contig",
icon = icon("calculator"),
style = "simple",
color = "danger",
block = TRUE, size = "lg")
),
column(12,
tags$hr(
style = ("border-top: 2px
hidden #A9A9A9;")),
),
column(12,
column(3,
tags$p(tagList(icon("caret-right"),
"Output Directory:"),
style = "font-size: 20px;
font-weight: bold;"),
),
column(9,
h4(shinyDirectory),
)
),
column(12,
column(3,
tags$p(
tagList(icon("caret-right"),
"Raw ABI Parent Directory: "),
style = "font-size: 20px;
font-weight: bold;"),
),
column(9,
h4(SangerAlignment@
ABIF_Directory),
)
),
column(12,
column(3,
tags$p(
tagList(icon("caret-right"),
"Consenesus Read Name:"),
style = "font-size: 20px;
font-weight: bold;"),
),
column(9,
h4(contigParam[["contigName"]]),
)
),
column(12,
column(3,
tags$p(
tagList(icon("caret-right"),
"Forward Suffix RegExp:"),
style = "font-size: 20px;
font-weight: bold;"),
),
column(9,
h4(SangerAlignment@
REGEX_SuffixForward),
)
),
column(12,
column(3,
tags$p(
tagList(icon("caret-right"),
"Forward Read Number:"),
style = "font-size: 20px;
font-weight: bold;"),
),
column(9,
h4(length(SangerAlignment@
contigList[[contigIndex]]@
forwardReadList)),
)
),
column(12,
column(3,
tags$p(
tagList(icon("caret-right"),
"Reverse Suffix RegExp:"),
style = "font-size: 20px;
font-weight: bold;"),
),
column(9,
h4(SangerAlignment@
REGEX_SuffixReverse),
)
),
column(12,
column(3,
tags$p(
tagList(icon("caret-right"),
"Reverse Read Number:"),
style = "font-size: 20px;
font-weight: bold;"),
),
column(9,
h4(length(SangerAlignment@
contigList[[contigIndex]]@
reverseReadList)),
)
),
),
################################################
#### Add this after having reference sample ####
################################################
tags$hr(style = ("border-top: 4px hidden #A9A9A9;")),
box(title = tags$p("Contig Parameters",
style = "font-size: 24px;
font-weight: bold;"),
collapsible = TRUE,
status = "success", width = 12,
column(4,
uiOutput("SAMinReadsNum") ,
),
column(4,
uiOutput("SAMinReadLength") ,
),
column(4,
uiOutput("SAMinFractionCall") ,
),
column(4,
uiOutput("SAMaxFractionLost") ,
),
column(4,
uiOutput("SAAcceptStopCodons") ,
),
column(4,
uiOutput("SAReadingFrame") ,
),
),
box(title = tags$p("Genetic Code Data Frame",
style = "font-size: 24px;
font-weight: bold;"),
collapsible = TRUE,
status = "success", width = 12,
column(width = 2,
tags$p("Tri-nucleotide:",
style = "font-size: 15px;
font-weight: bold;"),
tags$p("Amino Acid : ",
style = "font-size: 15px;
font-weight: bold;"),
tags$p("('*' : stop codon) ",
style = "font-size: 12px;
font-weight: italic;"),
),
column(width = 10,
excelOutput("geneticCodeDF",
width = "100%",
height = "50"),
style = paste("height:100%; ",
"overflow-y: hidden;",
"overflow-x: scroll;")
),
),
uiOutput("SArefAminoAcidSeq") ,
),
box(title = tags$p(tagList(icon("dot-circle"),
"Consensus Read Results: "),
style = "font-size: 26px;
font-weight: bold;"),
solidHeader = TRUE, collapsible = TRUE,
status = "success", width = 12,
tags$hr(style =("border-top: 4px hidden #A9A9A9;")),
box(title = tags$p("Alignment",
style = "font-size: 24px;
font-weight: bold;"),
collapsible = TRUE,
status = "success", width = 12,
column(width = 12,
htmlOutput("contigAlignmentHTML"),
),
),
box(title = tags$p("Differences Data frame",
style = "font-size: 24px;
font-weight: bold;"),
collapsible = TRUE,
status = "success", width = 12,
column(width = 12,
# uiOutput("SADifferencesDFUI"),
dataTableOutput("SADifferencesDF"),
style =
paste("height:100%; overflow-y:",
"scroll;overflow-x: scroll;")
)
),
box(title = tags$p("Dendrogram",
style = "font-size: 24px;
font-weight: bold;"),
collapsible = TRUE,
status = "success", width = 12,
column(width = 12,
plotOutput("dendrogramPlot"),
style =
paste("height:100%; overflow-y:",
"scroll;overflow-x: scroll;")
),
column(width = 12,
tags$hr(
style =("border-top: 4px hidden #A9A9A9;")),
),
column(width = 12,
dataTableOutput("dendrogramDF"),
style =
paste("height:100%; overflow-y:",
"scroll;overflow-x: scroll;")
)
),
box(title = tags$p("Samples Distance",
style = "font-size: 24px;
font-weight: bold;"),
collapsible = TRUE,
status = "success", width = 12,
column(width = 12,
# plot()
# uiOutput("SADistanceMatrixPlotUI"),
plotlyOutput("SADistanceMatrixPlot"),
style =
paste("height:100%; overflow-y:",
"scroll;overflow-x: scroll;")
),
column(width = 12,
tags$hr(
style =("border-top: 4px hidden #A9A9A9;")),
),
column(width = 12,
# uiOutput("SADistanceMatrixUI"),
dataTableOutput("SADistanceMatrix"),
style =
paste("height:100%; overflow-y:",
"scroll;overflow-x: scroll;")
)
),
box(title = tags$p("Indels Data frame",
style = "font-size: 24px;
font-weight: bold;"),
collapsible = TRUE,
status = "success", width = 12,
column(width = 12,
# uiOutput("SAIndelsDFUI"),
dataTableOutput("SAIndelsDF"),
style =
paste("height:100%; overflow-y:",
"scroll;overflow-x: scroll;")
)
),
box(title = tags$p("Stop Codons Data frame",
style = "font-size: 24px;
font-weight: bold;"),
collapsible = TRUE,
status = "success", width = 12,
column(width = 12,
# uiOutput("SAStopCodonsDFUI"),
dataTableOutput("SAStopCodonsDF"),
style =
paste("height:100%; overflow-y:",
"scroll;overflow-x: scroll;")
)
)
)
)
} else if (!is.na(strtoi(sidebar_menu[[1]])) &&
sidebar_menu[[2]] == "Contig" &&
sidebar_menu[[3]] == "-" &&
!is.na(strtoi(sidebar_menu[[4]])) &&
(sidebar_menu[[5]] == "Forward" ||
sidebar_menu[[5]] == "Reverse") &&
sidebar_menu[[6]] == "Read") {
contigIndex <- strtoi(sidebar_menu[[1]])
readIndex <- strtoi(sidebar_menu[[4]])
directionParam <- sidebar_menu[[5]]
if (directionParam == "Forward") {
sequenceParam[["primarySeq"]] <<-
as.character(SangerAlignment@
contigList[[contigIndex]]@
forwardReadList[[readIndex]]@primarySeq)
sequenceParam[["secondarySeq"]] <<-
as.character(SangerAlignment@
contigList[[contigIndex]]@
forwardReadList[[readIndex]]@secondarySeq)
sequenceParam[["primaryAASeqS1"]] <<-
as.character(SangerAlignment@
contigList[[contigIndex]]@
forwardReadList[[readIndex]]@primaryAASeqS1)
sequenceParam[["primaryAASeqS2"]] <<-
as.character(SangerAlignment@
contigList[[contigIndex]]@
forwardReadList[[readIndex]]@primaryAASeqS2)
sequenceParam[["primaryAASeqS3"]] <<-
as.character(SangerAlignment@
contigList[[contigIndex]]@
forwardReadList[[readIndex]]@primaryAASeqS3)
trimmedParam[["M1TrimmingCutoff"]] <<-
SangerAlignment@
contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@
M1TrimmingCutoff
trimmedParam[["M2CutoffQualityScore"]] <<-
SangerAlignment@
contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@
M2CutoffQualityScore
trimmedParam[["M2SlidingWindowSize"]] <<-
SangerAlignment@
contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@
M2SlidingWindowSize
trimmedRV[["rawSeqLength"]] <<-
SangerAlignment@
contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@rawSeqLength
trimmedRV[["rawMeanQualityScore"]] <<-
SangerAlignment@
contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@
rawMeanQualityScore
trimmedRV[["rawMinQualityScore"]] <<-
SangerAlignment@
contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@rawMinQualityScore
trimmedRV[["trimmedStartPos"]] <<-
SangerAlignment@
contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@trimmedStartPos
trimmedRV[["trimmedFinishPos"]] <<-
SangerAlignment@
contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@trimmedFinishPos
trimmedRV[["trimmedSeqLength"]] <<-
SangerAlignment@
contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@trimmedSeqLength
trimmedRV[["trimmedMeanQualityScore"]] <<-
SangerAlignment@
contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@
trimmedMeanQualityScore
trimmedRV[["trimmedMinQualityScore"]] <<-
SangerAlignment@
contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@
trimmedMinQualityScore
trimmedRV[["remainingRatio"]] <<-
round(SangerAlignment@
contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@
remainingRatio * 100, 2)
ChromatogramParam[["baseNumPerRow"]] <<-
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@ChromatogramParam@
baseNumPerRow
ChromatogramParam[["heightPerRow"]] <<-
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@ChromatogramParam@
heightPerRow
ChromatogramParam[["signalRatioCutoff"]] <<-
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@ChromatogramParam@
signalRatioCutoff
ChromatogramParam[["showTrimmed"]] <<-
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@ChromatogramParam@
showTrimmed
SangerReadBFN <-
basename(SangerAlignment@
contigList[[contigIndex]]@
forwardReadList[[readIndex]]@readFileName)
SangerReadAFN <-
SangerAlignment@
contigList[[contigIndex]]@
forwardReadList[[readIndex]]@readFileName
} else if (directionParam == "Reverse") {
sequenceParam[["primarySeq"]] <<-
as.character(SangerAlignment@
contigList[[contigIndex]]@
reverseReadList[[readIndex]]@primarySeq)
sequenceParam[["secondarySeq"]] <<-
as.character(SangerAlignment@
contigList[[contigIndex]]@
reverseReadList[[readIndex]]@secondarySeq)
sequenceParam[["primaryAASeqS1"]] <<-
as.character(SangerAlignment@
contigList[[contigIndex]]@
reverseReadList[[readIndex]]@primaryAASeqS1)
sequenceParam[["primaryAASeqS2"]] <<-
as.character(SangerAlignment@
contigList[[contigIndex]]@
reverseReadList[[readIndex]]@primaryAASeqS2)
sequenceParam[["primaryAASeqS3"]] <<-
as.character(SangerAlignment@
contigList[[contigIndex]]@
reverseReadList[[readIndex]]@primaryAASeqS3)
trimmedParam[["M1TrimmingCutoff"]] <<-
SangerAlignment@
contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@
M1TrimmingCutoff
trimmedParam[["M2CutoffQualityScore"]] <<-
SangerAlignment@
contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@
M2CutoffQualityScore
trimmedParam[["M2SlidingWindowSize"]] <<-
SangerAlignment@
contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@
M2SlidingWindowSize
trimmedRV[["rawSeqLength"]] <<-
SangerAlignment@
contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@rawSeqLength
trimmedRV[["rawMeanQualityScore"]] <<-
SangerAlignment@
contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@
rawMeanQualityScore
trimmedRV[["rawMinQualityScore"]] <<-
SangerAlignment@
contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@rawMinQualityScore
trimmedRV[["trimmedStartPos"]] <<-
SangerAlignment@
contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@trimmedStartPos
trimmedRV[["trimmedFinishPos"]] <<-
SangerAlignment@
contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@trimmedFinishPos
trimmedRV[["trimmedSeqLength"]] <<-
SangerAlignment@
contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@trimmedSeqLength
trimmedRV[["trimmedMeanQualityScore"]] <<-
SangerAlignment@
contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@
trimmedMeanQualityScore
trimmedRV[["trimmedMinQualityScore"]] <<-
SangerAlignment@
contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@
trimmedMinQualityScore
trimmedRV[["remainingRatio"]] <<-
round(SangerAlignment@
contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@
remainingRatio * 100, 2)
ChromatogramParam[["baseNumPerRow"]] <<-
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@ChromatogramParam@
baseNumPerRow
ChromatogramParam[["heightPerRow"]] <<-
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@ChromatogramParam@
heightPerRow
ChromatogramParam[["signalRatioCutoff"]] <<-
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@ChromatogramParam@
signalRatioCutoff
ChromatogramParam[["showTrimmed"]] <<-
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@ChromatogramParam@
showTrimmed
SangerReadBFN <-
basename(SangerAlignment@
contigList[[contigIndex]]@
reverseReadList[[readIndex]]@readFileName)
SangerReadAFN <-
SangerAlignment@
contigList[[contigIndex]]@
reverseReadList[[readIndex]]@readFileName
}
log_info(">>>>>>>> Inside '", input$sidebar_menu, "'")
h1(input$sidebar_menu)
fluidRow(
useShinyjs(),
box(title = tags$p(tagList(icon("dot-circle"),
"Raw File: "),
style = "font-size: 26px;
font-weight: bold;"),
solidHeader = TRUE,
status = "success", width = 12,
h1(SangerReadBFN),
tags$h5(paste("( full path:",
SangerReadAFN,
")"), style = "font-style:italic")),
box(title = tags$p(
tagList(icon("dot-circle"),
"Primary, Secondary DNA Sequences & Amino Acid Sequence (Before Trimming):"),
style = "font-size: 26px;
font-weight: bold;"),
solidHeader = TRUE, collapsible = TRUE,
status = "success", width = 12,
tags$hr(style = ("border-top: 4px hidden #A9A9A9;")),
column(width = 12,
tags$p(tagList(icon("bars"),
"Primary Sequence"),
style = "font-size: 22px;
font-weight: bold;"),
excelOutput("primarySeqDF",
width = "100%", height = "50"),
tags$br(),
tags$br(),
tags$p(tagList(icon("bars"),
"Secondary Sequence"),
style = "font-size: 22px;
font-weight: bold;"),
excelOutput("secondSeqDF",
width = "100%", height = "50"),
tags$br(),
tags$br(),
tags$p(tagList(icon("bars"),
"Quality Phred Score"),
style = "font-size: 22px;
font-weight: bold;"),
excelOutput("qualityScoreDF",
width = "100%", height = "50"),
style = paste("overflow-y: hidden;",
"overflow-x: scroll;")
),
),
box(title = tags$p(tagList(icon("dot-circle"),
"Quality Report: "),
style = "font-size: 26px;
font-weight: bold;"),
solidHeader = TRUE, collapsible = TRUE,
status = "success", width = 12,
tags$hr(
style = ("border-top: 4px hidden #A9A9A9;")),
box(title =
tags$p(tagList(icon("arrow-circle-right"),
"Trimming Parameters Input"),
style = "font-size: 24px;
font-weight: bold;"),
collapsible = TRUE,
status = "success", width = 12,
fluidRow(
column(width = 12,
uiOutput("TrimmingMethodSelectionOutput"),
),
),
column(width = 12,
uiOutput("TrimmingMethodUI"),
),
actionBttn("startTrimmingButton",
"Apply Trimming Parameters",
style = "simple", color = "danger",
block = TRUE, size = "lg")
),
box(title = tags$p(tagList(icon("arrow-circle-left"),
"Trimmed Result Output"),
style = "font-size: 24px;
font-weight: bold;"),
collapsible = TRUE,
status = "success", width = 12,
fluidRow(
box(title = tags$p("Before Trimming",
style = "font-size: 21px;
font-weight: bold;"),
collapsible = TRUE,
status = "success", width = 12,
column(width = 12,
column(4,
uiOutput("rawSeqLength") ,
),
column(4,
uiOutput("rawMeanQualityScore"),
),
column(4,
uiOutput("rawMinQualityScore"),
),
),
),
),
fluidRow(
box(title = tags$p("After Trimming",
style = "font-size: 21px;
font-weight: bold;"),
collapsible = TRUE,
status = "success", width = 12,
column(width = 12,
column(4,
uiOutput("trimmedSeqLength"),
),
column(4,
uiOutput("trimmedMeanQualityScore"),
),
column(4,
uiOutput("trimmedMinQualityScore"),
),
),
column(width = 12,
column(4,
uiOutput("trimmedStartPos") ,
),
column(4,
uiOutput("trimmedFinishPos") ,
),
column(4,
uiOutput("remainingRatio") ,
)
),
),
),
tags$hr(
style = ("border-top: 6px double #A9A9A9;")),
fluidRow(
box(title = tags$p("Quality Trimming Plot",
style = "font-size: 21px;
font-weight: bold;"),
collapsible = TRUE,
status = "success", width = 12,
plotlyOutput("qualityQualityBasePlot") %>%
withSpinner()),
),
),
),
box(title =
tags$p(tagList(icon("dot-circle"),
"DNA Sequence
(After Trimming):"),
style = "font-size: 26px;
font-weight: bold;"),
solidHeader = TRUE, collapsible = TRUE,
status = "success", width = 12,
tags$hr(style = ("border-top: 4px hidden #A9A9A9;")),
column(width = 12,
tags$p(tagList(icon("bars"),
"Primary Sequence"),
style = "font-size: 22px;
font-weight: bold;"),
excelOutput("primarySeqTrimmedDF",
width = "100%", height = "50"),
tags$br(),
tags$br(),
tags$p(tagList(icon("bars"),
"Secondary Sequence"),
style = "font-size: 22px;
font-weight: bold;"),
excelOutput("secondSeqTrimmedDF",
width = "100%", height = "50"),
tags$br(),
tags$br(),
tags$p(tagList(icon("bars"),
"Quality Phred Score"),
style = "font-size: 22px;
font-weight: bold;"),
excelOutput("qualityScoreTrimmedDF",
width = "100%", height = "50"),
tags$br(),
tags$br(),
tags$p(tagList(icon("bars"),
"AA Sequence 1"),
style = "font-size: 22px;
font-weight: bold;"),
excelOutput("PrimAASeqS1DF",
width = "100%", height = "50"),
tags$br(),
tags$br(),
tags$p(tagList(icon("bars"),
"AA Sequence 2"),
style = "font-size: 22px;
font-weight: bold;"),
excelOutput("PrimAASeqS2DF",
width = "100%", height = "50"),
tags$br(),
tags$br(),
tags$p(tagList(icon("bars"),
"AA Sequence 3"),
style = "font-size: 22px;
font-weight: bold;"),
excelOutput("PrimAASeqS3DF",
width = "100%", height = "50"),
style = paste("overflow-y: hidden;",
"overflow-x: scroll;")
)
),
box(title = tags$p(tagList(icon("dot-circle"),
"Chromatogram: "),
style = "font-size: 26px;
font-weight: bold;"),
solidHeader = TRUE, collapsible = TRUE,
status = "success", width = 12,
tags$hr(style = ("border-top: 4px hidden #A9A9A9;")),
box(title = tags$p(tagList(icon("arrow-circle-right"),
"Chromatogram Input"),
style = "font-size: 24px;
font-weight: bold;"),
collapsible = TRUE,
status = "success", width = 12,
column(3,
sliderInput("ChromatogramBasePerRow",
label = h4("Base Number Per Row"),
min = 5,
max = 200,
value = ChromatogramParam[["baseNumPerRow"]]),
sliderInput("ChromatogramHeightPerRow",
label = h4("Height Per Row"),
min = 50,
max = 600,
value =ChromatogramParam[["heightPerRow"]]),
),
column(3,
numericInput(
"ChromatogramSignalRatioCutoff",
h3("Signal Ratio Cutoff"),
value = ChromatogramParam[["signalRatioCutoff"]]),
checkboxInput(
"ChromatogramCheckShowTrimmed",
"Show trimmed region",
value = ChromatogramParam[["showTrimmed"]])
),
column(3,
uiOutput("ChromatogramtrimmedStartPos"),
),
column(3,
uiOutput("ChromatogramtrimmedFinishPos"),
),
actionBttn("saveChromatogramParam",
"Apply Chromatogram Parameters",
style = "simple", color = "danger",
block = TRUE, size = "lg")
),
box(title = tags$p(tagList(icon("arrow-circle-left"),
"Chromatogram Output"),
style = "font-size: 24px;
font-weight: bold;"),
collapsible = TRUE,
status = "success", width = 12,
column(width = 12,
uiOutput("chromatogramUIOutput"),
)
),
)
)
}
})
############################################################################
### All other features (dynamic header / button save / button close)
############################################################################
observeEvent(input$sidebar_menu, {
sidebar_menu <- tstrsplit(input$sidebar_menu, " ")
if (sidebar_menu[[1]] == "Contigs" &&
sidebar_menu[[2]] == "Alignment" &&
sidebar_menu[[3]] == "Overview" &&
sidebar_menu[[4]] == "Page" &&
sidebar_menu[[5]] == "_") {
shinyjs::html("rightHeader", "SangerAlignment Overview Page")
} else if (!is.na(strtoi(sidebar_menu[[1]])) &&
sidebar_menu[[2]] == "Sanger" &&
sidebar_menu[[3]] == "Contig" &&
sidebar_menu[[4]] == "Overview" &&
sidebar_menu[[5]] == "Page") {
contigIndex <- strtoi(sidebar_menu[[1]])
shinyjs::html("rightHeader", paste(contigIndex, "SangerContig Overview Page"))
} else if (!is.na(strtoi(sidebar_menu[[1]])) &&
sidebar_menu[[2]] == "Contig" &&
sidebar_menu[[3]] == "-" &&
!is.na(strtoi(sidebar_menu[[4]])) &&
(sidebar_menu[[5]] == "Forward" ||
sidebar_menu[[5]] == "Reverse") &&
sidebar_menu[[6]] == "Read") {
contigIndex <- strtoi(sidebar_menu[[1]])
readIndex <- strtoi(sidebar_menu[[4]])
directionParam <- sidebar_menu[[5]]
shinyjs::html("rightHeader",
paste(contigIndex, "SangerContig -",
readIndex, directionParam,
"SangerRead", "Page"))
}
})
### ------------------------------------------------------------------------
### observeEvent: Adding dynamic sidebar
### ------------------------------------------------------------------------
# !!! Fix !!!
dynamicMenuSideBarSA(input, output, session, SangerAlignmentParam)
############################################################################
### All other features (dynamic header / button save / button close)
############################################################################
### ------------------------------------------------------------------------
### observeEvent: Button Close UI
### ------------------------------------------------------------------------
observeEvent(input$closeUI, {
log_info("@@@@@@@ 'close button' has been clicked")
btn <- input$closeUI
stopApp()
})
### ------------------------------------------------------------------------
### observeEvent: Button Save S4 object
### ------------------------------------------------------------------------
observeEvent(input$saveS4, {
shinyjs::disable("closeUI")
shinyjs::disable("saveS4")
log_info("@@@@@@@ 'save button' has been clicked")
newS4Object <- file.path(shinyDirectory,
"SangerAlignment.Rda")
showNotification(
ui = column(12,
tags$p(tagList(icon("dot-circle"),
"New S4 object is store as: "),
style = "font-size: 28px;
font-weight: bold;"),
tags$p(paste0("'", newS4Object, "'"),
style = "font-size: 26px;
font-style: italic"),
tags$br(),
tags$p(">> Run",
style = "font-size: 18px;
font-style: italic"),
tags$p(paste0("readRDS(\"",newS4Object,
"\")"),
style = "font-size: 18px;
font-weight: bold;
font-family: Courier, Monospace;"),
tags$p(" to load saved S4 object into R
environment",
style = "font-size: 18px;
font-style: italic")),
closeButton = TRUE, id = "saveNotification",
type = "message", duration = 10)
### --------------------------------------------------------------------
### Save SangerContig quality S4 object
### --------------------------------------------------------------------
saveRDS(SangerAlignment, file=newS4Object)
log_info("New S4 object is store as: ", newS4Object)
NEW_SANGER_ALIGNED_CONSENSUS_READ_SET <<- readRDS(file=newS4Object)
shinyjs::enable("saveS4")
shinyjs::enable("closeUI")
})
### ------------------------------------------------------------------------
### observeEvent: Button contigs alignment re-calculating (SA) UI
### ------------------------------------------------------------------------
observeEvent(input$recalculateButtonSA, {
shinyjs::disable("closeUI")
shinyjs::disable("recalculateButtonSA")
log_info("######## Reactive button clicked !!!")
log_info("######## Start re-aligning contigs")
if (input$sidebar_menu == "Contigs Alignment Overview Page _") {
CSSetResult <-
alignContigs (SangerAlignment@contigList,
SangerAlignment@geneticCode,
SangerAlignment@refAminoAcidSeq,
SangerAlignment@contigList[[1]]@minFractionCall,
SangerAlignment@contigList[[1]]@maxFractionLost,
1)
SangerAlignment@contigsConsensus <<- CSSetResult$consensus
SangerAlignment@contigsAlignment <<- CSSetResult$aln
SangerAlignment@contigsTree <<- CSSetResult$aln.tree
sangerAlignmentParam[["contigsConsensus"]] <<- SangerAlignment@contigsConsensus
sangerAlignmentParam[["contigsAlignment"]] <<- as.character(SangerAlignment@contigsAlignment)
sangerAlignmentParam[["contigsTree"]] <<- SangerAlignment@contigsTree
log_info("######## Finish contigs re-alignment")
}
shinyjs::enable("recalculateButtonSA")
shinyjs::enable("closeUI")
})
### ------------------------------------------------------------------------
### observeEvent: Button SangerContig re-calculating (SA) UI
### ------------------------------------------------------------------------
observeEvent(input$recalculateButton, {
shinyjs::disable("closeUI")
shinyjs::disable("recalculateButton")
log_info("@@@@@@@ 'Reactive button' has been clicked")
log_info("######## Start recalculating contig")
sidebar_menu <- tstrsplit(input$sidebar_menu, " ")
contigIndex <- strtoi(sidebar_menu[[1]])
if (!is.na(contigIndex)) {
CSResult<-
calculateContigSeq (
SangerAlignment@contigList[[contigIndex]]@inputSource,
SangerAlignment@contigList[[contigIndex]]@forwardReadList,
SangerAlignment@contigList[[contigIndex]]@reverseReadList,
SangerAlignment@contigList[[contigIndex]]@refAminoAcidSeq,
SangerAlignment@contigList[[contigIndex]]@minFractionCall,
SangerAlignment@contigList[[contigIndex]]@maxFractionLost,
SangerAlignment@contigList[[contigIndex]]@geneticCode,
SangerAlignment@contigList[[contigIndex]]@acceptStopCodons,
SangerAlignment@contigList[[contigIndex]]@readingFrame)
SangerAlignment@contigList[[contigIndex]]@contigSeq <<- CSResult$consensusGapfree
SangerAlignment@contigList[[contigIndex]]@differencesDF <<- CSResult$diffsDf
SangerAlignment@contigList[[contigIndex]]@alignment <<- CSResult$aln2
SangerAlignment@contigList[[contigIndex]]@distanceMatrix <<- CSResult$dist
SangerAlignment@contigList[[contigIndex]]@dendrogram <<- CSResult$dend
SangerAlignment@contigList[[contigIndex]]@indelsDF <<- CSResult$indels
SangerAlignment@contigList[[contigIndex]]@stopCodonsDF <<- CSResult$stopsDf
SangerAlignment@contigList[[contigIndex]]@secondaryPeakDF <<- CSResult$spDf
contigParam[["contigSeq"]] <<- SangerAlignment@contigList[[contigIndex]]@contigSeq
contigParam[["differencesDF"]] <<- SangerAlignment@contigList[[contigIndex]]@differencesDF
contigParam[["alignment"]] <<- as.character(SangerAlignment@contigList[[contigIndex]]@alignment)
contigParam[["distanceMatrix"]] <<-SangerAlignment@contigList[[contigIndex]]@distanceMatrix
contigParam[["dendrogram"]] <<- SangerAlignment@contigList[[contigIndex]]@dendrogram
contigParam[["indelsDF"]] <<- SangerAlignment@contigList[[contigIndex]]@indelsDF
contigParam[["stopCodonsDF"]] <<- SangerAlignment@contigList[[contigIndex]]@stopCodonsDF
contigParam[["secondaryPeakDF"]] <<- SangerAlignment@contigList[[contigIndex]]@secondaryPeakDF
}
log_info("######## Finish recalculating contig")
shinyjs::enable("recalculateButton")
shinyjs::enable("closeUI")
})
### ------------------------------------------------------------------------
### observeEvent: Button apply trimming parameters
### ------------------------------------------------------------------------
observeEvent(input$startTrimmingButton, {
sidebar_menu <- tstrsplit(input$sidebar_menu, " ")
contigIndex <- strtoi(sidebar_menu[[1]])
readIndex <- strtoi(sidebar_menu[[4]])
directionParam <- sidebar_menu[[5]]
if (!is.na(contigIndex) &&
!is.na(readIndex)) {
if (directionParam == "Forward") {
activated_read_list <- SangerAlignment@contigList[[contigIndex]]@forwardReadList
} else if (directionParam == "Reverse") {
activated_read_list <- SangerAlignment@contigList[[contigIndex]]@reverseReadList
}
if (activated_read_list[[readIndex]]@QualityReport@TrimmingMethod == "M1") {
if (!is.na(as.numeric(input$M1TrimmingCutoffText)) &&
as.numeric(input$M1TrimmingCutoffText) > 0 &&
as.numeric(input$M1TrimmingCutoffText) <= 1) {
inputM1TrimmingCutoffText <- input$M1TrimmingCutoffText
} else {
inputM1TrimmingCutoffText <- 0.0001
}
if (directionParam == "Forward") {
trimmingPos <-
M1inside_calculate_trimming(
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@
qualityPhredScores,
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@
qualityBaseScores,
as.numeric(inputM1TrimmingCutoffText))
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@
M1TrimmingCutoff <<- as.numeric(inputM1TrimmingCutoffText)
trimmedParam[["M1TrimmingCutoff"]] <<-
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@M1TrimmingCutoff
} else if (directionParam == "Reverse") {
trimmingPos <-
M1inside_calculate_trimming(
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@
qualityPhredScores,
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@
qualityBaseScores,
as.numeric(inputM1TrimmingCutoffText))
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@
M1TrimmingCutoff <<- as.numeric(inputM1TrimmingCutoffText)
trimmedParam[["M1TrimmingCutoff"]] <<-
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@M1TrimmingCutoff
}
} else if (activated_read_list[[readIndex]]@QualityReport@TrimmingMethod == "M2") {
if (!is.na(strtoi(input$M2CutoffQualityScoreText)) &&
strtoi(input$M2CutoffQualityScoreText) > 0 &&
strtoi(input$M2CutoffQualityScoreText) <= 60 &&
strtoi(input$M2CutoffQualityScoreText) %% 1 ==0) {
inputM2CutoffQualityScoreText <- input$M2CutoffQualityScoreText
} else {
inputM2CutoffQualityScoreText <- 20
}
if (!is.na(strtoi(input$M2SlidingWindowSizeText)) &&
strtoi(input$M2SlidingWindowSizeText) > 0 &&
strtoi(input$M2SlidingWindowSizeText) <= 40 &&
strtoi(input$M2SlidingWindowSizeText) %% 1 ==0) {
inputM2SlidingWindowSizeText <- input$M2SlidingWindowSizeText
} else {
inputM2SlidingWindowSizeText <- 10
}
if (directionParam == "Forward") {
trimmingPos <-
M2inside_calculate_trimming(
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@
qualityPhredScores,
strtoi(inputM2CutoffQualityScoreText),
strtoi(inputM2SlidingWindowSizeText)
)
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@
M2CutoffQualityScore <<- strtoi(inputM2CutoffQualityScoreText)
trimmedParam[["M2CutoffQualityScore"]] <<-
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@
M2CutoffQualityScore
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@
M2SlidingWindowSize <<- strtoi(inputM2SlidingWindowSizeText)
trimmedParam[["M2SlidingWindowSize"]] <<-
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@
M2SlidingWindowSize
} else if ("Reverse") {
trimmingPos <-
M2inside_calculate_trimming(
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@
qualityPhredScores,
strtoi(inputM2CutoffQualityScoreText),
strtoi(inputM2SlidingWindowSizeText)
)
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@
M2CutoffQualityScore <<- strtoi(inputM2CutoffQualityScoreText)
trimmedParam[["M2CutoffQualityScore"]] <<-
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@
M2CutoffQualityScore
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@
M2SlidingWindowSize <<- strtoi(inputM2SlidingWindowSizeText)
trimmedParam[["M2SlidingWindowSize"]] <<-
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@
M2SlidingWindowSize
}
}
if (directionParam == "Forward") {
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@
rawSeqLength <<- trimmingPos[["rawSeqLength"]]
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@
rawMeanQualityScore <<- trimmingPos[["rawMeanQualityScore"]]
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@
rawMinQualityScore <<- trimmingPos[["rawMinQualityScore"]]
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@
trimmedStartPos <<- trimmingPos[["trimmedStartPos"]]
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@
trimmedFinishPos <<- trimmingPos[["trimmedFinishPos"]]
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@
trimmedSeqLength <<- trimmingPos[["trimmedSeqLength"]]
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@
trimmedMeanQualityScore <<- trimmingPos[["trimmedMeanQualityScore"]]
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@
trimmedMinQualityScore <<- trimmingPos[["trimmedMinQualityScore"]]
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@
remainingRatio <<- trimmingPos[["remainingRatio"]]
trimmedRV[["rawSeqLength"]] <<-
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@rawSeqLength
trimmedRV[["rawMeanQualityScore"]] <<-
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@
rawMeanQualityScore
trimmedRV[["rawMinQualityScore"]] <<-
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@rawMinQualityScore
trimmedRV[["trimmedStartPos"]] <<-
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@trimmedStartPos
trimmedRV[["trimmedFinishPos"]] <<-
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@trimmedFinishPos
trimmedRV[["trimmedSeqLength"]] <<-
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@trimmedSeqLength
trimmedRV[["trimmedMeanQualityScore"]] <<-
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@
trimmedMeanQualityScore
trimmedRV[["trimmedMinQualityScore"]] <<-
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@
trimmedMinQualityScore
trimmedRV[["remainingRatio"]] <<-
round(SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@
remainingRatio * 100, 2)
} else if (directionParam == "Reverse") {
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@
rawSeqLength <<- trimmingPos[["rawSeqLength"]]
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@
rawMeanQualityScore <<- trimmingPos[["rawMeanQualityScore"]]
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@
rawMinQualityScore <<- trimmingPos[["rawMinQualityScore"]]
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@
trimmedStartPos <<- trimmingPos[["trimmedStartPos"]]
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@
trimmedFinishPos <<- trimmingPos[["trimmedFinishPos"]]
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@
trimmedSeqLength <<- trimmingPos[["trimmedSeqLength"]]
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@
trimmedMeanQualityScore <<- trimmingPos[["trimmedMeanQualityScore"]]
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@
trimmedMinQualityScore <<- trimmingPos[["trimmedMinQualityScore"]]
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@
remainingRatio <<- trimmingPos[["remainingRatio"]]
trimmedRV[["rawSeqLength"]] <<-
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@rawSeqLength
trimmedRV[["rawMeanQualityScore"]] <<-
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@
rawMeanQualityScore
trimmedRV[["rawMinQualityScore"]] <<-
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@rawMinQualityScore
trimmedRV[["trimmedStartPos"]] <<-
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@trimmedStartPos
trimmedRV[["trimmedFinishPos"]] <<-
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@trimmedFinishPos
trimmedRV[["trimmedSeqLength"]] <<-
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@trimmedSeqLength
trimmedRV[["trimmedMeanQualityScore"]] <<-
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@
trimmedMeanQualityScore
trimmedRV[["trimmedMinQualityScore"]] <<-
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@
trimmedMinQualityScore
trimmedRV[["remainingRatio"]] <<-
round(SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@
remainingRatio * 100, 2)
}
}
})
### ------------------------------------------------------------------------
### observeEvent: Button chromatogram parameters re-calculating UI
### ------------------------------------------------------------------------
observeEvent(input$saveChromatogramParam, {
sidebar_menu <- tstrsplit(input$sidebar_menu, " ")
contigIndex <- strtoi(sidebar_menu[[1]])
readIndex <- strtoi(sidebar_menu[[4]])
directionParam <- sidebar_menu[[5]]
### ------------------------------------------------------------
### Update ChromatogramBasePerRow
### ------------------------------------------------------------
if (!is.na(contigIndex) &&
!is.na(readIndex)) {
if (directionParam == "Forward") {
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@ChromatogramParam@
baseNumPerRow <<- input$ChromatogramBasePerRow
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@ChromatogramParam@
heightPerRow <<- input$ChromatogramHeightPerRow
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@ChromatogramParam@
signalRatioCutoff <<- input$ChromatogramSignalRatioCutoff
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@ChromatogramParam@
showTrimmed <<- input$ChromatogramCheckShowTrimmed
} else if (directionParam == "Reverse") {
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@ChromatogramParam@
baseNumPerRow <<- input$ChromatogramBasePerRow
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@ChromatogramParam@
heightPerRow <<- input$ChromatogramHeightPerRow
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@ChromatogramParam@
signalRatioCutoff <<- input$ChromatogramSignalRatioCutoff
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@ChromatogramParam@
showTrimmed <<- input$ChromatogramCheckShowTrimmed
}
### ----------------------------------------------------------------
### Save 'ChromatogramParam' dynamic value
### ----------------------------------------------------------------
ChromatogramParam[["baseNumPerRow"]] <<-
input$ChromatogramBasePerRow
ChromatogramParam[["heightPerRow"]] <<-
input$ChromatogramHeightPerRow
ChromatogramParam[["signalRatioCutoff"]] <<-
input$ChromatogramSignalRatioCutoff
ChromatogramParam[["showTrimmed"]] <<-
input$ChromatogramCheckShowTrimmed
}
})
############################################################################
### SangerAlignment
############################################################################
### ------------------------------------------------------------------------
### Alignment
### ------------------------------------------------------------------------
output$sangerAlignmentAlignmentHTML<-renderUI({
if (input$sidebar_menu == "Contigs Alignment Overview Page _") {
browseSeqHTML <-
file.path(shinyDirectory,
"_SangerAlignment_BrowseSeqs.html")
if (!identical(sangerAlignmentParam[["contigsAlignment"]], character(0))) {
BrowseSeqs(DNAStringSet(sangerAlignmentParam[["contigsAlignment"]]) ,
openURL=FALSE, htmlFile=browseSeqHTML)
}
log_info("file.exists(browseSeqHTML): ", file.exists(browseSeqHTML))
log_info("(browseSeqHTML): ", (browseSeqHTML))
if (file.exists(browseSeqHTML)) {
column(width = 12,
includeHTML(browseSeqHTML),
style = paste("height:100%; ",
"overflow-y: hidden;",
"overflow-x: scroll;")
)
} else {
h4("*** The number of contigs is less than 2.
sCannot create 'BrowseSeqs' alignment. ***",
style="font-weight: bold; font-style: italic;")
}
}
})
### ------------------------------------------------------------------------
### Contigs Tree
### ------------------------------------------------------------------------
output$SATreePlotUI <- renderUI({
if (input$sidebar_menu == "Contigs Alignment Overview Page _") {
if (sangerAlignmentParam[["contigsTree"]]$tip.label != '' &&
!is.null(sangerAlignmentParam[["contigsTree"]]$tip.label)) {
plotOutput("SATreePlot")
} else {
h4("*** The number of contigs is less than 3 or quality of reads are too low.
'Contigs Tree' cannot be created. ***",
style="font-weight: bold; font-style: italic;")
}
}
})
output$SATreePlot <- renderPlot({
if (input$sidebar_menu == "Contigs Alignment Overview Page _") {
plot(sangerAlignmentParam[["contigsTree"]])
}
})
############################################################################
### SangerContig / SangerAlignment Share
############################################################################
### ------------------------------------------------------------------------
### genetic code
### ------------------------------------------------------------------------
output$geneticCodeDF <- renderExcel({
SAGeneticCode <- SangerAlignment@geneticCode
suppressMessages(
excelTable(data = t(data.frame(SAGeneticCode)),
defaultColWidth = 50, editable = FALSE, rowResize = FALSE,
columnResize = FALSE, allowInsertRow = FALSE,
allowInsertColumn = FALSE, allowDeleteRow = FALSE,
allowDeleteColumn = FALSE, allowRenameColumn = FALSE)
)
})
### ------------------------------------------------------------------------
### refAminoAcidSeq
### ------------------------------------------------------------------------
output$SArefAminoAcidSeq <- renderUI({
if (SangerAlignment@refAminoAcidSeq == "") {
box(title = tags$p("Reference Amino Acid Sequence",
style = "font-size: 24px;
font-weight: bold;"),
collapsible = TRUE,
status = "success", width = 12,
column(width = 1),
column(width = 11,
h4("Reference Amino Acid Sequence is not provided."))
)
} else {
box(title = tags$p("Reference Amino Acid Sequence",
style = "font-size: 24px;
font-weight: bold;"),
collapsible = TRUE,
status = "success", width = 12,
column(width = 2,
tags$br(),
tags$p("AA Sequence:",
style = "font-size: 15px;
font-weight: bold;"),
),
column(width = 10,
excelOutput("SArefAminoAcidSeqDF",
width = "100%", height = "50"),
style = paste("height:100%; ",
"overflow-y: hidden;",
"overflow-x: scroll;")
),
)
}
})
output$SArefAminoAcidSeqDF <- renderExcel({
refAminoAcidSeqVec <-
strsplit(SangerAlignment@refAminoAcidSeq, "")[[1]]
names(refAminoAcidSeqVec) <- c(seq_len(length(refAminoAcidSeqVec)))
suppressMessages(
excelTable(data =
t(data.frame(refAminoAcidSeqVec)),
defaultColWidth = 50, editable = FALSE, rowResize = FALSE,
columnResize = FALSE, allowInsertRow = FALSE,
allowInsertColumn = FALSE, allowDeleteRow = FALSE,
allowDeleteColumn = FALSE, allowRenameColumn = FALSE)
)
})
############################################################################
### SangerContig
############################################################################
valueBoxSAMinReadsNum (input, output, SangerAlignment, session)
valueBoxSAMinReadLength (input, output, SangerAlignment, session)
valueBoxSAMinFractionCall (input, output, SangerAlignment, session)
valueBoxSAMaxFractionLost (input, output, SangerAlignment, session)
valueBoxSAAcceptStopCodons (input, output, SangerAlignment, session)
valueBoxSAReadingFrame (input, output, SangerAlignment, session)
### ------------------------------------------------------------------------
### Alignment
### ------------------------------------------------------------------------
output$contigAlignmentHTML<-renderUI({
sidebar_menu <- tstrsplit(input$sidebar_menu, " ")
contigIndex <- strtoi(sidebar_menu[[1]])
if (!is.na(contigIndex)) {
browseSeqHTML <-
file.path(shinyDirectory, "BrowseSeqs_html",
paste0(sidebar_menu[[1]], "_",
contigParam[["contigName"]],
"_Alignment_BrowseSeqs.html"))
if (!dir.exists(file.path(shinyDirectory, "BrowseSeqs_html"))) {
dir.create(file.path(shinyDirectory, "BrowseSeqs_html"))
}
BrowseSeqs(DNAStringSet(contigParam[["alignment"]]),
openURL=FALSE, htmlFile=browseSeqHTML)
column(width = 12,
includeHTML(browseSeqHTML),
style = paste("height:100%; ",
"overflow-y: hidden;",
"overflow-x: scroll;")
)
}
})
### ------------------------------------------------------------------------
### difference
### ------------------------------------------------------------------------
output$SADifferencesDFUI <- renderUI({
sidebar_menu <- tstrsplit(input$sidebar_menu, " ")
contigIndex <- strtoi(sidebar_menu[[1]])
if (!is.na(contigIndex)) {
if (all(dim(contigParam[["differencesDF"]]) == c(0,0))) {
h4("*** 'Differences' dataframe is empty. ***",
style="font-weight: bold; font-style: italic;")
} else {
dataTableOutput("SADifferencesDF")
}
}
})
output$SADifferencesDF = renderDataTable({
contigParam[["differencesDF"]]
})
### ------------------------------------------------------------------------
### dendrogram
### ------------------------------------------------------------------------
output$dendrogramPlot <- renderPlot({
sidebar_menu <- tstrsplit(input$sidebar_menu, " ")
contigIndex <- strtoi(sidebar_menu[[1]])
if (!is.na(contigIndex)) {
ggdendrogram(contigParam[["dendrogram"]][[2]], rotate = TRUE)
}
})
output$dendrogramDF <- renderDataTable({
sidebar_menu <- tstrsplit(input$sidebar_menu, " ")
contigIndex <- strtoi(sidebar_menu[[1]])
if (!is.na(contigIndex)) {
contigParam[["dendrogram"]][[1]]
}
})
### ------------------------------------------------------------------------
### distance
### ------------------------------------------------------------------------
output$SADistanceMatrixPlotUI <- renderUI({
sidebar_menu <- tstrsplit(input$sidebar_menu, " ")
contigIndex <- strtoi(sidebar_menu[[1]])
if (!is.na(contigIndex)) {
if (all(dim(contigParam[["distanceMatrix"]]) == c(0,0))) {
h4("*** 'Distance' dataframe is empty. (Cannot plot)***",
style="font-weight: bold; font-style: italic;")
} else {
plotlyOutput("SADistanceMatrixPlot")
}
}
})
output$SADistanceMatrixPlot <- renderPlotly({
sidebar_menu <- tstrsplit(input$sidebar_menu, " ")
contigIndex <- strtoi(sidebar_menu[[1]])
if (!is.na(contigIndex)) {
SangerReadBFN <-
SangerAlignmentParam[[contigIndex]]$SangerReadBFN
suppressPlotlyMessage(
plot_ly(x = SangerReadBFN,
y = SangerReadBFN,
z = contigParam[["distanceMatrix"]],
colors = colorRamp(c("white", "#32a852")),
type = "heatmap")
)
}
})
output$SADistanceMatrixUI <- renderUI({
sidebar_menu <- tstrsplit(input$sidebar_menu, " ")
contigIndex <- strtoi(sidebar_menu[[1]])
if (!is.na(contigIndex)) {
if (all(dim(contigParam[["distanceMatrix"]]) == c(0,0))) {
h4("*** 'Distance' dataframe is empty. ***",
style="font-weight: bold; font-style: italic;")
} else {
dataTableOutput("SADistanceMatrix")
}
}
})
output$SADistanceMatrix = renderDataTable({
contigParam[["distanceMatrix"]]
})
### ------------------------------------------------------------------------
### SAIndelsDF
### ------------------------------------------------------------------------
output$SAIndelsDFUI <- renderUI({
sidebar_menu <- tstrsplit(input$sidebar_menu, " ")
contigIndex <- strtoi(sidebar_menu[[1]])
if (!is.na(contigIndex)) {
if (all(dim(contigParam[["indelsDF"]] ) == c(0,0))) {
h4("*** 'Indels' data frame is empty. ***",
style="font-weight: bold; font-style: italic;")
} else {
dataTableOutput("SAIndelsDF")
}
}
})
output$SAIndelsDF <- renderDataTable({
contigParam[["indelsDF"]]
})
### ------------------------------------------------------------------------
### SAStopCodons
### ------------------------------------------------------------------------
output$SAStopCodonsDFUI <- renderUI({
sidebar_menu <- tstrsplit(input$sidebar_menu, " ")
contigIndex <- strtoi(sidebar_menu[[1]])
if (!is.na(contigIndex)) {
if (all(dim(contigParam[["stopCodonsDF"]]) == c(0,0))) {
h4("*** 'Stop Codons' dataframe is empty. ***",
style="font-weight: bold; font-style: italic;")
} else {
dataTableOutput("SAStopCodonsDF")
}
}
})
output$SAStopCodonsDF <- renderDataTable({
contigParam[["stopCodonsDF"]]
})
############################################################################
### SangerRead (Function for singel read in contigSeq)
############################################################################
output$primarySeqDF <- renderExcel({
sidebar_menu <- tstrsplit(input$sidebar_menu, " ")
contigIndex <- strtoi(sidebar_menu[[1]])
readIndex <- strtoi(sidebar_menu[[4]])
directionParam <- sidebar_menu[[5]]
if (!is.na(contigIndex) &&
!is.na(readIndex)) {
primarySeqDisplay (sequenceParam, colors=colors)
}
})
output$secondSeqDF <- renderExcel({
sidebar_menu <- tstrsplit(input$sidebar_menu, " ")
contigIndex <- strtoi(sidebar_menu[[1]])
readIndex <- strtoi(sidebar_menu[[4]])
directionParam <- sidebar_menu[[5]]
if (!is.na(contigIndex) &&
!is.na(readIndex)) {
secondarySeqDisplay (sequenceParam, colors=colors)
}
})
output$qualityScoreDF <- renderExcel({
sidebar_menu <- tstrsplit(input$sidebar_menu, " ")
contigIndex <- strtoi(sidebar_menu[[1]])
readIndex <- strtoi(sidebar_menu[[4]])
directionParam <- sidebar_menu[[5]]
if (!is.na(contigIndex) &&
!is.na(readIndex)) {
if (directionParam == "Forward") {
PhredScore <-
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@
QualityReport@qualityPhredScores
} else if (directionParam == "Reverse") {
PhredScore <-
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@
QualityReport@qualityPhredScores
}
qualityScoreDisplay (PhredScore)
}
})
output$PrimAASeqS1DF <- renderExcel({
sidebar_menu <- tstrsplit(input$sidebar_menu, " ")
contigIndex <- strtoi(sidebar_menu[[1]])
readIndex <- strtoi(sidebar_menu[[4]])
directionParam <- sidebar_menu[[5]]
if (!is.na(contigIndex) &&
!is.na(readIndex)) {
PrimAASeqS1Display (sequenceParam)
}
})
output$PrimAASeqS2DF <- renderExcel({
sidebar_menu <- tstrsplit(input$sidebar_menu, " ")
contigIndex <- strtoi(sidebar_menu[[1]])
readIndex <- strtoi(sidebar_menu[[4]])
directionParam <- sidebar_menu[[5]]
if (!is.na(contigIndex) &&
!is.na(readIndex)) {
PrimAASeqS2Display (sequenceParam)
}
})
output$PrimAASeqS3DF <- renderExcel({
sidebar_menu <- tstrsplit(input$sidebar_menu, " ")
contigIndex <- strtoi(sidebar_menu[[1]])
readIndex <- strtoi(sidebar_menu[[4]])
directionParam <- sidebar_menu[[5]]
if (!is.na(contigIndex) &&
!is.na(readIndex)) {
PrimAASeqS3Display (sequenceParam)
}
})
output$primarySeqTrimmedDF <- renderExcel({
sidebar_menu <- tstrsplit(input$sidebar_menu, " ")
contigIndex <- strtoi(sidebar_menu[[1]])
readIndex <- strtoi(sidebar_menu[[4]])
directionParam <- sidebar_menu[[5]]
if (!is.na(contigIndex) &&
!is.na(readIndex)) {
primarySeqTrimmedDisplay (input, output, session,
sequenceParam, trimmedRV, colors=colors)
}
})
output$secondSeqTrimmedDF <- renderExcel({
sidebar_menu <- tstrsplit(input$sidebar_menu, " ")
contigIndex <- strtoi(sidebar_menu[[1]])
readIndex <- strtoi(sidebar_menu[[4]])
directionParam <- sidebar_menu[[5]]
if (!is.na(contigIndex) &&
!is.na(readIndex)) {
secondSeqTrimmedDisplay (input, output, session,
sequenceParam, trimmedRV, colors=colors)
}
})
output$qualityScoreTrimmedDF <- renderExcel({
sidebar_menu <- tstrsplit(input$sidebar_menu, " ")
contigIndex <- strtoi(sidebar_menu[[1]])
readIndex <- strtoi(sidebar_menu[[4]])
directionParam <- sidebar_menu[[5]]
if (!is.na(contigIndex) &&
!is.na(readIndex)) {
if (directionParam == "Forward") {
PhredScore <-
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@
QualityReport@qualityPhredScores[
(trimmedRV[["trimmedStartPos"]]+1):
trimmedRV[["trimmedFinishPos"]]]
} else if (directionParam == "Reverse") {
PhredScore <-
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@
QualityReport@qualityPhredScores[
(trimmedRV[["trimmedStartPos"]]+1):
trimmedRV[["trimmedFinishPos"]]]
}
qualityScoreDisplay (PhredScore)
}
})
############################################################################
### Trimming method selection functions
############################################################################
### ------------------------------------------------------------------------
### Trimming Method Selection (Just check forward reads => not dynamic)
### ------------------------------------------------------------------------
output$TrimmingMethodSelectionOutput <- renderUI({
sidebar_menu <- tstrsplit(input$sidebar_menu, " ")
contigIndex <- strtoi(sidebar_menu[[1]])
readIndex <- strtoi(sidebar_menu[[4]])
if (!is.na(contigIndex) &&
!is.na(readIndex)) {
if (SangerAlignment@contigList[[contigIndex]]@forwardReadList[[readIndex]]@QualityReport@TrimmingMethod == "M1") {
tagList(icon("check-circle"),
"Your trimming method selection :
'Modified Mott Trimming'")
} else if (SangerAlignment@contigList[[contigIndex]]@forwardReadList[[readIndex]]@QualityReport@TrimmingMethod == "M2") {
tagList(icon("check-circle"),
"Your trimming method selection :
'Trimmomatics Sliding Window Trimming'")
}
}
})
output$TrimmingMethodUI <- renderUI({
sidebar_menu <- tstrsplit(input$sidebar_menu, " ")
contigIndex <- strtoi(sidebar_menu[[1]])
readIndex <- strtoi(sidebar_menu[[4]])
directionParam <- sidebar_menu[[5]]
if (!is.na(contigIndex) &&
!is.na(readIndex)) {
if (directionParam == "Forward") {
activated_read_list <- SangerAlignment@contigList[[contigIndex]]@forwardReadList
} else if (directionParam == "Reverse") {
activated_read_list <- SangerAlignment@contigList[[contigIndex]]@reverseReadList
}
if (activated_read_list[[readIndex]]@QualityReport@TrimmingMethod == "M1") {
if (directionParam == "Forward") {
if (is.null(SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@
QualityReport@M1TrimmingCutoff)) {
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@
QualityReport@M1TrimmingCutoff <<- 0.0001
}
} else if (directionParam == "Reverse") {
if (is.null(SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@
QualityReport@M1TrimmingCutoff)) {
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@
QualityReport@M1TrimmingCutoff <<- 0.0001
}
}
fluidRow(
column(6,
uiOutput("M1TrimmingCutoff") ,
tags$ul(
textInput("M1TrimmingCutoffText",
label = p("Change Value"),
value = toString(
trimmedParam[["M1TrimmingCutoff"]]),
width = '70%')
),
),
)
} else if (activated_read_list[[readIndex]]@QualityReport@TrimmingMethod == "M2") {
if (directionParam == "Forward") {
if (is.null(SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@
QualityReport@M2CutoffQualityScore)) {
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@
QualityReport@M2CutoffQualityScore <<- 20
}
if (is.null(SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@
QualityReport@M2SlidingWindowSize )) {
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@
QualityReport@M2SlidingWindowSize <<- 10
}
} else if (directionParam == "Reverse") {
if (is.null(SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@
QualityReport@M2CutoffQualityScore)) {
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@
QualityReport@M2CutoffQualityScore <<- 20
}
if (is.null(SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@
QualityReport@M2SlidingWindowSize )) {
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@
QualityReport@M2SlidingWindowSize <<- 10
}
}
fluidRow(
column(6,
uiOutput("M2CutoffQualityScore") ,
tags$ul(
textInput("M2CutoffQualityScoreText",
label = p("Change Value"),
value = toString(
trimmedParam[["M2CutoffQualityScore"]]),
width = '70%')
),
),
column(6,
uiOutput("M2SlidingWindowSize") ,
tags$ul(
textInput("M2SlidingWindowSizeText",
label = p("Change Value"),
value = toString(
trimmedParam[["M2SlidingWindowSize"]]),
width = '70%')
),
),
)
}
}
})
valueBoxM1TrimmingCutoff (input, output, session)
valueBoxM2CutoffQualityScore (input, output, session)
valueBoxM2SlidingWindowSize (input, output, session)
valueBoxRawSeqLength (input, output, session, trimmedRV)
valueBoxRawMeanQualityScore (input, output, session, trimmedRV)
valueBoxRawMinQualityScore (input, output, session, trimmedRV)
valueBoxTrimmedStartPos (input, output, session, trimmedRV)
valueBoxTrimmedFinishPos (input, output, session, trimmedRV)
valueBoxTrimmedSeqLength (input, output, session, trimmedRV)
valueBoxTrimmedMeanQualityScore (input, output, session, trimmedRV)
valueBoxTrimmedMinQualityScore (input, output, session, trimmedRV)
valueBoxRemainingRatio (input, output, session, trimmedRV)
output$qualityQualityBasePlot <- renderPlotly({
sidebar_menu <- tstrsplit(input$sidebar_menu, " ")
contigIndex <- strtoi(sidebar_menu[[1]])
readIndex <- strtoi(sidebar_menu[[4]])
directionParam <- sidebar_menu[[5]]
if (!is.na(contigIndex) &&
!is.na(readIndex)) {
if (directionParam == "Forward") {
qualityPhredScores <-
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@
QualityReport@qualityPhredScores
} else if (directionParam == "Reverse") {
qualityPhredScores <-
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@
QualityReport@qualityPhredScores
}
qualityQualityBasePlotDisplay(input, output,session,
trimmedRV, qualityPhredScores)
}
})
valueBoxChromTrimmedStartPos (input, output, session, trimmedRV)
valueBoxChromTrimmedFinishPos (input, output, session, trimmedRV)
# chromatogram
output$chromatogramUIOutput <- renderUI({
sidebar_menu <- tstrsplit(input$sidebar_menu, " ")
contigIndex <- strtoi(sidebar_menu[[1]])
readIndex <- strtoi(sidebar_menu[[4]])
directionParam <- sidebar_menu[[5]]
if (sidebar_menu[[2]] == "Contig" &&
sidebar_menu[[3]] == "-" &&
!is.na(readIndex) &&
(directionParam == "Forward" ||
directionParam == "Reverse") &&
sidebar_menu[[6]] == "Read") {
trimmedRV[["trimmedSeqLength"]]
if (directionParam == "Forward") {
rawSeqLength <-
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@
QualityReport@rawSeqLength
trimmedSeqLength <-
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@
QualityReport@trimmedSeqLength
} else if (directionParam == "Reverse") {
rawSeqLength <-
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@
QualityReport@rawSeqLength
trimmedSeqLength <-
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@
QualityReport@trimmedSeqLength
}
chromatogramRowNumAns <- chromatogramRowNum (
strtoi(ChromatogramParam[["baseNumPerRow"]]),
rawSeqLength, trimmedSeqLength,
ChromatogramParam[["showTrimmed"]]) *
strtoi(ChromatogramParam[["heightPerRow"]])
plotOutput("chromatogram", height = chromatogramRowNumAns)
}
})
output$chromatogram <- renderPlot({
## !!!!! Update !!!!
shinyjs::disable("startTrimmingButton")
shinyjs::disable("saveChromatogramParam")
shinyjs::disable("ChromatogramBasePerRow")
shinyjs::disable("ChromatogramHeightPerRow")
shinyjs::disable("ChromatogramSignalRatioCutoff")
shinyjs::disable("ChromatogramCheckShowTrimmed")
shinyjs::disable("M1TrimmingCutoffText")
shinyjs::disable("M2CutoffQualityScoreText")
shinyjs::disable("M2SlidingWindowSizeText")
sidebar_menu <- tstrsplit(input$sidebar_menu, " ")
contigIndex <- strtoi(sidebar_menu[[1]])
readIndex <- strtoi(sidebar_menu[[4]])
directionParam <- sidebar_menu[[5]]
if (sidebar_menu[[2]] == "Contig" &&
sidebar_menu[[3]] == "-" &&
!is.na(readIndex) &&
(directionParam == "Forward" ||
directionParam == "Reverse") &&
sidebar_menu[[6]] == "Read") {
removeNotification(id = "saveNotification")
showNotification(
ui = fluidRow(
column(1),
column(11,
tags$p(tagList(icon("hourglass-start"),
"Plotting Chromatogram ... "),
style = "font-size: 28px;
font-weight: bold;"),
tags$p(tagList(icon("dot-circle"),
"Base pairs per row : ",
ChromatogramParam[["baseNumPerRow"]]),
style = "font-size: 20px;
font-style: italic"),
tags$p(tagList(icon("dot-circle"),
"Height per row : ",
ChromatogramParam[["heightPerRow"]]),
style = "font-size: 20px;
font-style: italic"),
tags$p(tagList(icon("dot-circle"),
"Signal Ratio Cutoff : ",
ChromatogramParam[["signalRatioCutoff"]]),
style = "font-size: 20px;
font-style: italic"),
tags$p(tagList(icon("dot-circle"),
"Show trimmed : ",
ChromatogramParam[["showTrimmed"]]),
style = "font-size: 20px;
font-style: italic"),
tags$p("( If 'Signal Ratio Cutoff' is too small,
it would need more time to replot
the chromatogram)",
style = "font-size: 16px;
font-style: italic"),)
),
action = NULL, duration = NULL, closeButton = FALSE,
id = "chromatogramNotification",
type = "message")
if (directionParam == "Forward") {
rawSeqLength <-
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@rawSeqLength
log_info(">>>>>>>>>>>> Re-running 'MakeBaseCalls' function (forward)")
### ----------------------------------------------------------------
### Re-run 'MakeBaseCall' function
### ----------------------------------------------------------------
hetcalls <-
MakeBaseCalls(SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]],
signalRatioCutoff = as.numeric(
ChromatogramParam[["signalRatioCutoff"]]))
### ----------------------------------------------------------------
### Update 'SangerContig'!
### ----------------------------------------------------------------
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@peakPosMatrix <<-
hetcalls@peakPosMatrix
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@peakAmpMatrix <<-
hetcalls@peakAmpMatrix
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@primarySeq <<-
hetcalls@primarySeq
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@secondarySeq <<-
hetcalls@secondarySeq
### ----------------------------------------------------------------
### Updating AASeqs
### ----------------------------------------------------------------
AASeqResult <- calculateAASeq (hetcalls@primarySeq,
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@trimmedStartPos,
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@QualityReport@trimmedFinishPos,
SangerAlignment@geneticCode)
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@primaryAASeqS1 <<-
AASeqResult[["primaryAASeqS1"]]
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@primaryAASeqS2 <<-
AASeqResult[["primaryAASeqS2"]]
SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@primaryAASeqS3 <<-
AASeqResult[["primaryAASeqS3"]]
### ----------------------------------------------------------------
### Updating reactive values
### ----------------------------------------------------------------
sequenceParam[["primarySeq"]] <<-
as.character(SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@primarySeq)
sequenceParam[["secondarySeq"]] <<-
as.character(SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@secondarySeq)
sequenceParam[["primaryAASeqS1"]] <<-
as.character(SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@primaryAASeqS1)
sequenceParam[["primaryAASeqS2"]] <<-
as.character(SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@primaryAASeqS2)
sequenceParam[["primaryAASeqS3"]] <<-
as.character(SangerAlignment@contigList[[contigIndex]]@
forwardReadList[[readIndex]]@primaryAASeqS3)
} else if (directionParam == "Reverse") {
rawSeqLength <-
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@rawSeqLength
log_info(">>>>>>>>>>>> Re-running 'MakeBaseCalls' function (reverse)")
### ----------------------------------------------------------------
### Re-run 'MakeBaseCall' function
### ----------------------------------------------------------------
hetcalls <-
MakeBaseCalls(SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]],
signalRatioCutoff = as.numeric(
ChromatogramParam[["signalRatioCutoff"]]))
### ------------------------------------------------------------
### Update 'SangerContig'!
### ------------------------------------------------------------
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@peakPosMatrix <<-
hetcalls@peakPosMatrix
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@peakAmpMatrix <<-
hetcalls@peakAmpMatrix
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@primarySeq <<-
hetcalls@primarySeq
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@secondarySeq <<-
hetcalls@secondarySeq
### ------------------------------------------------------------
### Updating AASeqs
### ------------------------------------------------------------
AASeqResult <- calculateAASeq (hetcalls@primarySeq,
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@trimmedStartPos,
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@QualityReport@trimmedFinishPos,
SangerAlignment@geneticCode)
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@primaryAASeqS1 <<-
AASeqResult[["primaryAASeqS1"]]
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@primaryAASeqS2 <<-
AASeqResult[["primaryAASeqS2"]]
SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@primaryAASeqS3 <<-
AASeqResult[["primaryAASeqS3"]]
### ------------------------------------------------------------
### Updating reactive values
### ------------------------------------------------------------
sequenceParam[["primarySeq"]] <<-
as.character(SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@primarySeq)
sequenceParam[["secondarySeq"]] <<-
as.character(SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@secondarySeq)
sequenceParam[["primaryAASeqS1"]] <<-
as.character(SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@primaryAASeqS1)
sequenceParam[["primaryAASeqS2"]] <<-
as.character(SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@primaryAASeqS2)
sequenceParam[["primaryAASeqS3"]] <<-
as.character(SangerAlignment@contigList[[contigIndex]]@
reverseReadList[[readIndex]]@primaryAASeqS3)
}
# log_info(">>>>>>>>>>>> 'MakeBaseCalls' finished")
chromatogram_overwrite(hetcalls,
width = strtoi(
ChromatogramParam[["baseNumPerRow"]]),
height = 2,
trim5 = trimmedRV[["trimmedStartPos"]],
trim3 = rawSeqLength -
trimmedRV[["trimmedFinishPos"]],
showtrim = (ChromatogramParam[["showTrimmed"]]),
showcalls = "both", colors = colors)
removeNotification(id = "chromatogramNotification")
shinyjs::enable("ChromatogramBasePerRow")
shinyjs::enable("ChromatogramHeightPerRow")
shinyjs::enable("ChromatogramSignalRatioCutoff")
shinyjs::enable("ChromatogramCheckShowTrimmed")
shinyjs::enable("M1TrimmingCutoffText")
shinyjs::enable("M2CutoffQualityScoreText")
shinyjs::enable("M2SlidingWindowSizeText")
shinyjs::enable("startTrimmingButton")
shinyjs::enable("saveChromatogramParam")
}
})
}
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