R/HTML.R
In 47Lies/isoformnspectRe: Companion package of a nextflow pipeline
Defines functions
HTML_VECTOR_Peptide2Popover
HTML_PrettyBlastSequence
HTML_Pretty_Sequence
UpdateSequence
HTML_HandleEndOfLine
Documented in
HTML_HandleEndOfLine
HTML_PrettyBlastSequence
HTML_Pretty_Sequence
HTML_VECTOR_Peptide2Popover
UpdateSequence
#' HTML_HandleEndOfLine add a end of a line
#'
#' @param EndOfTheLine At what position you are at the end of this line
#' @param LineWidth The length of the line
#'
#' @return charater chain with
#' @export
#'
#' @examples
#' HTML_HandleEndOfLine(EndOfTheLine=277,LineWidth=60)
HTML_HandleEndOfLine <- function(EndOfTheLine, LineWidth) {
if ((EndOfTheLine %% LineWidth) == 0) {
BeginingOfTheLine <- EndOfTheLine - LineWidth
} else{
##Case where the modulo is lesser than 10
# 966
#
if ((EndOfTheLine %% LineWidth) < 10) {
return("")
}
BeginingOfTheLine <- EndOfTheLine - EndOfTheLine %% LineWidth
}
ThicksValues <- seq(BeginingOfTheLine + 10, EndOfTheLine, 10)
NbBlocks <- length(ThicksValues)
OneChunk <- paste0(c(rep(" ", 9), "|"), collapse = "")
LineChunks <- paste0(rep(OneChunk, NbBlocks), collapse = " ")
LineValues <- formatC(x = ThicksValues, width = 10, flag = " ")
LineValues <- gsub(" ", " ", LineValues)
LineValues <- paste(LineValues, collapse = " ")
ReturnLine <-
paste(
"</br><mark class='position'>",
LineChunks,
"</br>",
LineValues,
"</br></br></mark>",
sep = ""
)
return(ReturnLine)
}
#' UpdateSequence Transform a AA sequence to a HTML ready to print string
#'
#' @param IR Integer Ranges with all necessay informations
#' @param PROTEIN_AA AA sequence
#'
#'
#' @export
#'
#' @return a string with span tag
#'
UpdateSequence<-function(IR,PROTEIN_AA){
INFOS<-data.frame(IR)
PROTEIN_AA[INFOS$start]<-paste(INFOS$Start.Prefix, PROTEIN_AA[INFOS$start], INFOS$Start.Suffix, sep="")
PROTEIN_AA[INFOS$end]<-paste(INFOS$End.Prefix, PROTEIN_AA[INFOS$end], INFOS$End.Suffix, sep="")
return(PROTEIN_AA)
}
#' HTML_Pretty_Sequence Prepare an HTML ready
#'
#' @param Sequence String of the protein AA Sequence
#' @param Peptides data.frame of the peptides attributed to this protein
#' @param Rescue Not Used for now
#' @param PerfectIsoformName Name of the Isoform as observed in the
#' @param LineWidth Number of AA before a new line (will not include the space inside)
#'
#' @return HTML string of the sequence embedded with features included as span
#' @import IRanges
#' @import GenomicRanges
#' @export
#'
#' @examples
#' library(Biostrings)
#' PB_FilePath <- system.file("extdata",
#' "protein_bank.example.fasta",
#' package = "isoformnspectRe")
#' ProteinBank<-readAAStringSet(
#' PB_FilePath
#' )
#' Sequence <- as.vector(ProteinBank["Example"])
#' Peptides <- data.frame(
#' Start = c(2, 2, 240),
#' End = c(10, 11, 253),
#' Pep = c(1.9437e-06, 0.00014334, 0.0001654),
#' Proteins = c(
#' "strngt.11487.1 Q8WUM4-3 strngt.11487.3 strngt.11487.2",
#' "strngt.11487.1 Q8WUM4-3 strngt.11487.3 strngt.11487.2",
#' "strngt.11487.2"),
#' Sequence = c("ATFISVQLK", "ATFISVQLKK", "YFYFQEVFPVLAAK ")
#' )
#' Sequence <- HTML_Pretty_Sequence(Sequence,Peptides)
HTML_Pretty_Sequence <- function(Sequence,
Peptides,
Rescue = NULL,
PerfectIsoformName = NULL,
LineWidth = 60) {
#Protein IntegerRange
LocalProteinSequence <-
unlist(strsplit(x = as.vector(Sequence), split = ""))
LocalProteinLength <- length(LocalProteinSequence)
Protein.IR <- IRanges::IRanges(start = 1, end = LocalProteinLength)
GenomicRanges::mcols(Protein.IR) <- data.frame(
Class = "Protein",
Start.Prefix = "<div style=\"font-family:monospace;font-size:16px;height:100%;overflow-y:scroll;\">",
Start.Suffix = "",
End.Prefix = "",
End.Suffix = paste(
HTML_HandleEndOfLine(LocalProteinLength,
LineWidth),
"</div>"
)
)
if (!is.null(PerfectIsoformName)) {
UNIPROTIsoformName <-
gsub(".*\\|([^\\|]*)-([^\\|]+)\\|.*",
"\\1-\\2",
PerfectIsoformName)
#SplicingVariations IntegerRange
SplicingVariations.IR <- GetRangesFromUniprot(UNIPROTIsoformName)
##Case Where the original sequence ends after the isoform sequence
# Q69JNO-3 VSP_058760
if (sum(!SplicingVariations.IR %within% Protein.IR)) {
end(SplicingVariations.IR)[end(SplicingVariations.IR) > LocalProteinLength] <-
LocalProteinLength
}
} else{
SplicingVariations.IR <- GetEmptySpanRanges()
}
#Newline IntegerRange
if (LocalProteinLength > LineWidth) {
NewLines <- seq(LineWidth, LocalProteinLength, LineWidth)
NewLines <- NewLines[!NewLines %in% LocalProteinLength]
NewLines.AfterChar <-
unlist(lapply(NewLines, function(x)
HTML_HandleEndOfLine(x, LineWidth)))
NewLines.IR <- IRanges::IRanges(start = NewLines, end = NewLines)
GenomicRanges::mcols(NewLines.IR) <- data.frame(
Class = "Newline",
Start.Prefix = "",
Start.Suffix = "",
End.Prefix = "",
End.Suffix = NewLines.AfterChar
)
} else{
NewLines.IR <- IRanges::IRanges()
NewLines <- c()
}
#Block IntegerRange
BlocksPosition <- seq(10, LocalProteinLength, 10)
BlocksPosition <- BlocksPosition[!BlocksPosition %in% NewLines]
BlocksPosition.IR <-
IRanges::IRanges(start = BlocksPosition,
end = BlocksPosition)
GenomicRanges::mcols(BlocksPosition.IR) <- data.frame(
Class = "BlockEnd",
Start.Prefix = "",
Start.Suffix = "",
End.Prefix = "",
End.Suffix = " "
)
IDX_Shared <- grep(" ", Peptides$Proteins)
IDX_Proteotypic <- grep(" ", Peptides$Proteins, invert = TRUE)
#ProteotypicIntergerRange
SharedPeptides.IR <- IRanges::IRanges(start = Peptides$Start[IDX_Shared],
end = Peptides$End[IDX_Shared])
GenomicRanges::mcols(SharedPeptides.IR) <- data.frame(
Title = paste(
"Peptide: ",
Peptides$Sequence[IDX_Shared],
"(",
formatC(Peptides$Pep[IDX_Shared], digits = 2),
")\n",
sep = ""
),
Class = "Peptide"
)
#PeptidesIntergerRange
Proteotypic.IR <- IRanges::IRanges(start = Peptides$Start[IDX_Proteotypic],
end = Peptides$End[IDX_Proteotypic])
GenomicRanges::mcols(Proteotypic.IR) <-
data.frame(
Title = paste(
"Peptide: ",
Peptides$Sequence[IDX_Proteotypic],
"(",
formatC(Peptides$Pep[IDX_Proteotypic], digits = 2),
")\n",
sep = ""
),
Class = "Peptide Proteotypic"
)
Peptides.IR <- c(SharedPeptides.IR, Proteotypic.IR)
#Infos
SpanRanges <- c(SplicingVariations.IR, Peptides.IR)
SpanRanges <- CollapseSpanRanges(SpanRanges)
DisjoinSpanRange <- SplitSpanRanges(SpanRanges, NewLines.IR)
GenomicRanges::mcols(DisjoinSpanRange)$Start.Prefix <-
paste(
"<span class=\"",
GenomicRanges::mcols(DisjoinSpanRange)$Class,
"\" title=\"",
GenomicRanges::mcols(DisjoinSpanRange)$Title,
"\">",
sep = ""
)
GenomicRanges::mcols(DisjoinSpanRange)$Start.Suffix <- ""
GenomicRanges::mcols(DisjoinSpanRange)$End.Prefix <- ""
GenomicRanges::mcols(DisjoinSpanRange)$End.Suffix <- "</span>"
#Insert Newlines into Disjoin IntegerRange
NewLines.IR.ToHandle <- NewLines.IR
OverlapsWithNewline <-
data.frame(findOverlaps(DisjoinSpanRange, NewLines.IR.ToHandle))
while (dim(OverlapsWithNewline)[1] > 0) {
##Case where the a peptide end with a new line it created a span that did not close anywhere and in doing so make it all
if (end(DisjoinSpanRange[OverlapsWithNewline$queryHits[1]]) == end(NewLines.IR.ToHandle[OverlapsWithNewline$subjectHits[1]])) {
} else{
Before <- DisjoinSpanRange[OverlapsWithNewline$queryHits[1]]
After <- Before
end(Before) <-
start(NewLines.IR.ToHandle[OverlapsWithNewline$subjectHits[1]])
start(After) <-
end(NewLines.IR.ToHandle[OverlapsWithNewline$subjectHits[1]]) + 1
DisjoinSpanRange <-
DisjoinSpanRange[-OverlapsWithNewline$queryHits[1]]
DisjoinSpanRange <- c(DisjoinSpanRange, Before, After)
DisjoinSpanRange <- sort(DisjoinSpanRange)
}
NewLines.IR.ToHandle <-
NewLines.IR.ToHandle[-OverlapsWithNewline$subjectHits[1]]
OverlapsWithNewline <-
data.frame(findOverlaps(DisjoinSpanRange, NewLines.IR.ToHandle))
}
# mcols(DisjoinSpanRange)$Start.Prefix <- paste( "<span class=\"", mcols(DisjoinSpanRange)$Class,
# "\" title=\"", mcols(DisjoinSpanRange)$Title, "\">", sep = "")
GenomicRanges::mcols(DisjoinSpanRange)$Start.Prefix <-
paste(
"<span class=\"",
GenomicRanges::mcols(DisjoinSpanRange)$Class,
"\" data-toggle=\"popover\" data-html=\"true\" data-trigger=\"hover click\" data-placement=\"bottom\" title=\"Features\" data-content=\"",
GenomicRanges::mcols(DisjoinSpanRange)$Title,
"\">",
sep = ""
)
GenomicRanges::mcols(DisjoinSpanRange)$Start.Suffix <- ""
GenomicRanges::mcols(DisjoinSpanRange)$End.Prefix <- ""
GenomicRanges::mcols(DisjoinSpanRange)$End.Suffix <- "</span>"
LocalProteinSequence <-
UpdateSequence(BlocksPosition.IR, LocalProteinSequence)
LocalProteinSequence <-
UpdateSequence(DisjoinSpanRange, LocalProteinSequence)
LocalProteinSequence <-
UpdateSequence(NewLines.IR, LocalProteinSequence)
LocalProteinSequence <-
UpdateSequence(Protein.IR, LocalProteinSequence)
LocalProteinSequence <- paste(LocalProteinSequence, collapse = "")
return(LocalProteinSequence)
}
#' HTML_PrettyBlastSequence prepare and HTML ready string with some more informations
#'
#' @param Sequence String of the protein AA Sequence
#' @param Peptides data.frame of the peptides attributed to this protein
#' @param Rescue Not Used for now
#' @param LineWidth Number of AA before a new line (will not include the space inside)
#'
#' @return HTML string of the sequence embedded with features included as span
#' @import IRanges
#' @import GenomicRanges
#' @export
#'
#' @examples
#' library(Biostrings)
#' PB_FilePath <- system.file("extdata",
#' "protein_bank.example.fasta",
#' package = "isoformnspectRe")
#' ProteinBank<-readAAStringSet(
#' PB_FilePath
#' )
#' Sequence <- as.vector(ProteinBank["Example"])
#' Peptides <- data.frame(
#' Start = c(2, 2, 240),
#' End = c(10, 11, 253),
#' Pep = c(1.9437e-06, 0.00014334, 0.0001654),
#' Proteins = c(
#' "strngt.11487.1 Q8WUM4-3 strngt.11487.3 strngt.11487.2",
#' "strngt.11487.1 Q8WUM4-3 strngt.11487.3 strngt.11487.2",
#' "strngt.11487.2"),
#' Sequence = c("ATFISVQLK", "ATFISVQLKK", "YFYFQEVFPVLAAK ")
#' )
#' Sequence <- HTML_Pretty_Sequence(Sequence,Peptides)
HTML_PrettyBlastSequence<-function(
Sequence,
Peptides,
Rescue,
LineWidth=60){
#Protein IntegerRange
LocalProteinSequence <- unlist(strsplit(x = as.vector(Sequence), split = ""))
LocalProteinLength<-length(LocalProteinSequence)
Protein.IR <- IRanges(start = 1, end = LocalProteinLength)
mcols(Protein.IR) <- data.frame(
Class = "Protein",
Start.Prefix = "<div style=\"font-family:monospace;font-size:16px;height:100%;overflow-y:scroll;\">",
Start.Suffix = "",
End.Prefix = "",
End.Suffix = paste(
HTML_HandleEndOfLine(LocalProteinLength, LineWidth),
"</div>"
)
)
#Newline IntegerRange
if(LocalProteinLength>LineWidth){
NewLines<-seq(LineWidth,LocalProteinLength,LineWidth)
NewLines<-NewLines[!NewLines %in% LocalProteinLength]
NewLines.AfterChar<-unlist( lapply( NewLines, function(x) HTML_HandleEndOfLine(x,LineWidth)))
NewLines.IR<-IRanges( start=NewLines, end=NewLines)
mcols(NewLines.IR)<-data.frame(Class="Newline", Start.Prefix="",
Start.Suffix="", End.Prefix="", End.Suffix=NewLines.AfterChar)
}else{
NewLines.IR<-IRanges()
NewLines<-c()
}
#Block IntegerRange
BlocksPosition<-seq(10, LocalProteinLength, 10)
BlocksPosition<-BlocksPosition[!BlocksPosition %in% NewLines]
BlocksPosition.IR <- IRanges(start = BlocksPosition, end = BlocksPosition)
mcols(BlocksPosition.IR) <- data.frame(
Class = "BlockEnd",
Start.Prefix = "",
Start.Suffix = "",
End.Prefix = "",
End.Suffix = " "
)
#Blast differences
Blast.IR <- IRanges(start = Rescue$QueryStart,
end = Rescue$QueryEnd)
mcols(Blast.IR) <- data.frame(
Class = "Blast",
Title = paste(
Rescue$SubjectSeqId,
" from:",
Rescue$SubjectStart,
" to:",
Rescue$SubjectEnd,
" of: ",
Rescue$SubjectLength,
sep = ""
)
)
Diffs.IR<-CompareTwoSequences(as.vector(Rescue$QuerySequence),
as.vector(Rescue$SubjectSequence),
Rescue$QueryStart)
Blast.IR<-c(Blast.IR, Diffs.IR)
IDX_Shared <- grep(" ",Peptides$Proteins)
IDX_Proteotypic <- grep(" ",Peptides$Proteins,invert = TRUE)
#ProteotypicIntergerRange
SharedPeptides.IR <- IRanges(start = Peptides$Start[IDX_Shared],
end = Peptides$End[IDX_Shared])
mcols(SharedPeptides.IR) <- data.frame(
Title = paste(
"Peptide: ",
Peptides$Sequence[IDX_Shared],
"(",
formatC(Peptides$Pep[IDX_Shared], digits = 2),
")\n",
sep = ""
),
Class = "Peptide"
)
#PeptidesIntergerRange
Proteotypic.IR <- IRanges(start = Peptides$Start[IDX_Proteotypic],
end = Peptides$End[IDX_Proteotypic])
mcols(Proteotypic.IR) <- data.frame(
Title = paste(
"Peptide: ",
Peptides$Sequence[IDX_Proteotypic],
"(",
formatC(Peptides$Pep[IDX_Proteotypic], digits = 2),
")\n",
sep = ""
),
Class = "Peptide Proteotypic"
)
Peptides.IR<-c(SharedPeptides.IR,Proteotypic.IR)
#Infos
SpanRanges<-c(Blast.IR,Peptides.IR)
SpanRanges<-CollapseSpanRanges(SpanRanges)
DisjoinSpanRange<-SplitSpanRanges(SpanRanges,NewLines.IR)
mcols(DisjoinSpanRange)$Start.Prefix <- paste("<span class=\"", mcols(DisjoinSpanRange)$Class, "\" title=\"",
mcols(DisjoinSpanRange)$Title, "\">", sep = "")
mcols(DisjoinSpanRange)$Start.Suffix <- ""
mcols(DisjoinSpanRange)$End.Prefix <- ""
mcols(DisjoinSpanRange)$End.Suffix <- "</span>"
#Insert Newlines into Disjoin IntegerRange
NewLines.IR.ToHandle<-NewLines.IR
OverlapsWithNewline<-data.frame(findOverlaps(DisjoinSpanRange,NewLines.IR.ToHandle))
while(dim(OverlapsWithNewline)[1]>0){
##Case where the a peptide end with a new line it created a span that did not close anywhere and in doing so make it all
if (end(DisjoinSpanRange[OverlapsWithNewline$queryHits[1]])==end(NewLines.IR.ToHandle[OverlapsWithNewline$subjectHits[1]])) {
} else{
Before <- DisjoinSpanRange[OverlapsWithNewline$queryHits[1]]
After <- Before
end(Before) <- start(NewLines.IR.ToHandle[OverlapsWithNewline$subjectHits[1]])
start(After) <- end(NewLines.IR.ToHandle[OverlapsWithNewline$subjectHits[1]]) + 1
DisjoinSpanRange <- DisjoinSpanRange[-OverlapsWithNewline$queryHits[1]]
DisjoinSpanRange <- c(DisjoinSpanRange, Before, After)
DisjoinSpanRange <- sort(DisjoinSpanRange)
}
NewLines.IR.ToHandle<-NewLines.IR.ToHandle[-OverlapsWithNewline$subjectHits[1]]
OverlapsWithNewline<-data.frame(findOverlaps(DisjoinSpanRange,NewLines.IR.ToHandle))
}
# mcols(DisjoinSpanRange)$Start.Prefix <- paste( "<span class=\"", mcols(DisjoinSpanRange)$Class,
# "\" title=\"", mcols(DisjoinSpanRange)$Title, "\">", sep = "")
mcols(DisjoinSpanRange)$Start.Prefix <- paste("<span class=\"", mcols(DisjoinSpanRange)$Class,
"\" data-toggle=\"popover\" data-html=\"true\" data-trigger=\"hover click\" data-placement=\"bottom\" title=\"Features\" data-content=\"", mcols(DisjoinSpanRange)$Title, "\">", sep = "")
mcols(DisjoinSpanRange)$Start.Suffix <- ""
mcols(DisjoinSpanRange)$End.Prefix <- ""
mcols(DisjoinSpanRange)$End.Suffix <- "</span>"
LocalProteinSequence<-UpdateSequence(BlocksPosition.IR, LocalProteinSequence)
LocalProteinSequence<-UpdateSequence(DisjoinSpanRange, LocalProteinSequence)
LocalProteinSequence<-UpdateSequence(NewLines.IR, LocalProteinSequence)
LocalProteinSequence<-UpdateSequence(Protein.IR, LocalProteinSequence)
LocalProteinSequence<-paste(LocalProteinSequence, collapse="")
#Status
PeptideInSAAV <- FALSE
PeptideInInsertion <- FALSE
PeptideInDeletion <- FALSE
PeptideOutOfBlastSAAV <- FALSE
SAAV <- FALSE
Insertion <- FALSE
Deletion <- FALSE
if(sum(mcols(Blast.IR)$Class=="SAAV")>0){SAAV <- TRUE}
if(sum(mcols(Blast.IR)$Class=="Insertion")>0){Insertion <- TRUE}
if(sum(mcols(Blast.IR)$Class=="Deletion")>0){Deletion <- TRUE}
if(sum(Peptides.IR %over% Blast.IR[mcols(Blast.IR)$Class=="SAAV"])>0){ PeptideInSAAV <- TRUE}
if(sum(Peptides.IR %over% Blast.IR[mcols(Blast.IR)$Class=="Insertion"])>0){ PeptideInInsertion <- TRUE}
if(sum(Peptides.IR %over% Blast.IR[mcols(Blast.IR)$Class=="Deletion"])>0){ PeptideInDeletion <- TRUE}
if(sum(!Peptides.IR %over% Blast.IR)>0){ PeptideOutOfBlastSAAV <- TRUE}
return(list(SequenceInHTML=LocalProteinSequence,
SAAVxPep=PeptideInSAAV,
SAAV=SAAV,
InsertionxPep=PeptideInInsertion,
Insertion=Insertion,
DeletionxPep=PeptideInDeletion,
Deletion=Deletion,
OutOfBlast=PeptideOutOfBlastSAAV))
}
#' Alter a peptide sequence to have an harmonious presentation
#'
#' @param Sequences Vector of peptides Sequence
#' @param MaxNChar Maximum width size of the peptide
#' @return string vector as a HTML span to have shorter form
#' @export
#'
#' @examples
#' library("DT")
#' library("data.table")
#' P_FilePath <- system.file("extdata",
#' "peptides.example.txt",
#' package = "isoformnspectRe")
#' Peptides<-fread(
#' P_FilePath,
#' integer64="double")
#' Peptides<-Peptides[,c("Sequence",
#' "Start position","End position")]
#' datatable(Peptides)
#' Peptides$Sequence<-HTML_VECTOR_Peptide2Popover(Peptides$Sequence)
#' datatable(Peptides,escape=FALSE,
#' options=list(
#' drawCallback=JS(
#' paste("$('[data-toggle=\"popover\"]').popover({container: 'body'});")
#' )))
HTML_VECTOR_Peptide2Popover<-function(Sequences,MaxNChar=15){
Too_Long_Sequence_Lengths <- nchar(Sequences) > 15
Sequences[Too_Long_Sequence_Lengths] <- paste(
"<span data-toggle=\"popover\"
data-trigger=\"hover click\" data-placement=\"right\"
data-html=\"true\" data-delay={show: 500, hide: 100}
title=\"Proteins\" data-content=\"",
Sequences[Too_Long_Sequence_Lengths],"\">",
base::substr(Sequences[Too_Long_Sequence_Lengths],
1,MaxNChar-3),
"...</span>",sep="")
return(Sequences)
}
47Lies/isoformnspectRe documentation built on May 29, 2021, 3 p.m.
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Defines functions HTML_VECTOR_Peptide2Popover HTML_PrettyBlastSequence HTML_Pretty_Sequence UpdateSequence HTML_HandleEndOfLine
Documented in HTML_HandleEndOfLine HTML_PrettyBlastSequence HTML_Pretty_Sequence HTML_VECTOR_Peptide2Popover UpdateSequence
#' HTML_HandleEndOfLine add a end of a line
#'
#' @param EndOfTheLine At what position you are at the end of this line
#' @param LineWidth The length of the line
#'
#' @return charater chain with
#' @export
#'
#' @examples
#' HTML_HandleEndOfLine(EndOfTheLine=277,LineWidth=60)
HTML_HandleEndOfLine <- function(EndOfTheLine, LineWidth) {
if ((EndOfTheLine %% LineWidth) == 0) {
BeginingOfTheLine <- EndOfTheLine - LineWidth
} else{
##Case where the modulo is lesser than 10
# 966
#
if ((EndOfTheLine %% LineWidth) < 10) {
return("")
}
BeginingOfTheLine <- EndOfTheLine - EndOfTheLine %% LineWidth
}
ThicksValues <- seq(BeginingOfTheLine + 10, EndOfTheLine, 10)
NbBlocks <- length(ThicksValues)
OneChunk <- paste0(c(rep(" ", 9), "|"), collapse = "")
LineChunks <- paste0(rep(OneChunk, NbBlocks), collapse = " ")
LineValues <- formatC(x = ThicksValues, width = 10, flag = " ")
LineValues <- gsub(" ", " ", LineValues)
LineValues <- paste(LineValues, collapse = " ")
ReturnLine <-
paste(
"</br><mark class='position'>",
LineChunks,
"</br>",
LineValues,
"</br></br></mark>",
sep = ""
)
return(ReturnLine)
}
#' UpdateSequence Transform a AA sequence to a HTML ready to print string
#'
#' @param IR Integer Ranges with all necessay informations
#' @param PROTEIN_AA AA sequence
#'
#'
#' @export
#'
#' @return a string with span tag
#'
UpdateSequence<-function(IR,PROTEIN_AA){
INFOS<-data.frame(IR)
PROTEIN_AA[INFOS$start]<-paste(INFOS$Start.Prefix, PROTEIN_AA[INFOS$start], INFOS$Start.Suffix, sep="")
PROTEIN_AA[INFOS$end]<-paste(INFOS$End.Prefix, PROTEIN_AA[INFOS$end], INFOS$End.Suffix, sep="")
return(PROTEIN_AA)
}
#' HTML_Pretty_Sequence Prepare an HTML ready
#'
#' @param Sequence String of the protein AA Sequence
#' @param Peptides data.frame of the peptides attributed to this protein
#' @param Rescue Not Used for now
#' @param PerfectIsoformName Name of the Isoform as observed in the
#' @param LineWidth Number of AA before a new line (will not include the space inside)
#'
#' @return HTML string of the sequence embedded with features included as span
#' @import IRanges
#' @import GenomicRanges
#' @export
#'
#' @examples
#' library(Biostrings)
#' PB_FilePath <- system.file("extdata",
#' "protein_bank.example.fasta",
#' package = "isoformnspectRe")
#' ProteinBank<-readAAStringSet(
#' PB_FilePath
#' )
#' Sequence <- as.vector(ProteinBank["Example"])
#' Peptides <- data.frame(
#' Start = c(2, 2, 240),
#' End = c(10, 11, 253),
#' Pep = c(1.9437e-06, 0.00014334, 0.0001654),
#' Proteins = c(
#' "strngt.11487.1 Q8WUM4-3 strngt.11487.3 strngt.11487.2",
#' "strngt.11487.1 Q8WUM4-3 strngt.11487.3 strngt.11487.2",
#' "strngt.11487.2"),
#' Sequence = c("ATFISVQLK", "ATFISVQLKK", "YFYFQEVFPVLAAK ")
#' )
#' Sequence <- HTML_Pretty_Sequence(Sequence,Peptides)
HTML_Pretty_Sequence <- function(Sequence,
Peptides,
Rescue = NULL,
PerfectIsoformName = NULL,
LineWidth = 60) {
#Protein IntegerRange
LocalProteinSequence <-
unlist(strsplit(x = as.vector(Sequence), split = ""))
LocalProteinLength <- length(LocalProteinSequence)
Protein.IR <- IRanges::IRanges(start = 1, end = LocalProteinLength)
GenomicRanges::mcols(Protein.IR) <- data.frame(
Class = "Protein",
Start.Prefix = "<div style=\"font-family:monospace;font-size:16px;height:100%;overflow-y:scroll;\">",
Start.Suffix = "",
End.Prefix = "",
End.Suffix = paste(
HTML_HandleEndOfLine(LocalProteinLength,
LineWidth),
"</div>"
)
)
if (!is.null(PerfectIsoformName)) {
UNIPROTIsoformName <-
gsub(".*\\|([^\\|]*)-([^\\|]+)\\|.*",
"\\1-\\2",
PerfectIsoformName)
#SplicingVariations IntegerRange
SplicingVariations.IR <- GetRangesFromUniprot(UNIPROTIsoformName)
##Case Where the original sequence ends after the isoform sequence
# Q69JNO-3 VSP_058760
if (sum(!SplicingVariations.IR %within% Protein.IR)) {
end(SplicingVariations.IR)[end(SplicingVariations.IR) > LocalProteinLength] <-
LocalProteinLength
}
} else{
SplicingVariations.IR <- GetEmptySpanRanges()
}
#Newline IntegerRange
if (LocalProteinLength > LineWidth) {
NewLines <- seq(LineWidth, LocalProteinLength, LineWidth)
NewLines <- NewLines[!NewLines %in% LocalProteinLength]
NewLines.AfterChar <-
unlist(lapply(NewLines, function(x)
HTML_HandleEndOfLine(x, LineWidth)))
NewLines.IR <- IRanges::IRanges(start = NewLines, end = NewLines)
GenomicRanges::mcols(NewLines.IR) <- data.frame(
Class = "Newline",
Start.Prefix = "",
Start.Suffix = "",
End.Prefix = "",
End.Suffix = NewLines.AfterChar
)
} else{
NewLines.IR <- IRanges::IRanges()
NewLines <- c()
}
#Block IntegerRange
BlocksPosition <- seq(10, LocalProteinLength, 10)
BlocksPosition <- BlocksPosition[!BlocksPosition %in% NewLines]
BlocksPosition.IR <-
IRanges::IRanges(start = BlocksPosition,
end = BlocksPosition)
GenomicRanges::mcols(BlocksPosition.IR) <- data.frame(
Class = "BlockEnd",
Start.Prefix = "",
Start.Suffix = "",
End.Prefix = "",
End.Suffix = " "
)
IDX_Shared <- grep(" ", Peptides$Proteins)
IDX_Proteotypic <- grep(" ", Peptides$Proteins, invert = TRUE)
#ProteotypicIntergerRange
SharedPeptides.IR <- IRanges::IRanges(start = Peptides$Start[IDX_Shared],
end = Peptides$End[IDX_Shared])
GenomicRanges::mcols(SharedPeptides.IR) <- data.frame(
Title = paste(
"Peptide: ",
Peptides$Sequence[IDX_Shared],
"(",
formatC(Peptides$Pep[IDX_Shared], digits = 2),
")\n",
sep = ""
),
Class = "Peptide"
)
#PeptidesIntergerRange
Proteotypic.IR <- IRanges::IRanges(start = Peptides$Start[IDX_Proteotypic],
end = Peptides$End[IDX_Proteotypic])
GenomicRanges::mcols(Proteotypic.IR) <-
data.frame(
Title = paste(
"Peptide: ",
Peptides$Sequence[IDX_Proteotypic],
"(",
formatC(Peptides$Pep[IDX_Proteotypic], digits = 2),
")\n",
sep = ""
),
Class = "Peptide Proteotypic"
)
Peptides.IR <- c(SharedPeptides.IR, Proteotypic.IR)
#Infos
SpanRanges <- c(SplicingVariations.IR, Peptides.IR)
SpanRanges <- CollapseSpanRanges(SpanRanges)
DisjoinSpanRange <- SplitSpanRanges(SpanRanges, NewLines.IR)
GenomicRanges::mcols(DisjoinSpanRange)$Start.Prefix <-
paste(
"<span class=\"",
GenomicRanges::mcols(DisjoinSpanRange)$Class,
"\" title=\"",
GenomicRanges::mcols(DisjoinSpanRange)$Title,
"\">",
sep = ""
)
GenomicRanges::mcols(DisjoinSpanRange)$Start.Suffix <- ""
GenomicRanges::mcols(DisjoinSpanRange)$End.Prefix <- ""
GenomicRanges::mcols(DisjoinSpanRange)$End.Suffix <- "</span>"
#Insert Newlines into Disjoin IntegerRange
NewLines.IR.ToHandle <- NewLines.IR
OverlapsWithNewline <-
data.frame(findOverlaps(DisjoinSpanRange, NewLines.IR.ToHandle))
while (dim(OverlapsWithNewline)[1] > 0) {
##Case where the a peptide end with a new line it created a span that did not close anywhere and in doing so make it all
if (end(DisjoinSpanRange[OverlapsWithNewline$queryHits[1]]) == end(NewLines.IR.ToHandle[OverlapsWithNewline$subjectHits[1]])) {
} else{
Before <- DisjoinSpanRange[OverlapsWithNewline$queryHits[1]]
After <- Before
end(Before) <-
start(NewLines.IR.ToHandle[OverlapsWithNewline$subjectHits[1]])
start(After) <-
end(NewLines.IR.ToHandle[OverlapsWithNewline$subjectHits[1]]) + 1
DisjoinSpanRange <-
DisjoinSpanRange[-OverlapsWithNewline$queryHits[1]]
DisjoinSpanRange <- c(DisjoinSpanRange, Before, After)
DisjoinSpanRange <- sort(DisjoinSpanRange)
}
NewLines.IR.ToHandle <-
NewLines.IR.ToHandle[-OverlapsWithNewline$subjectHits[1]]
OverlapsWithNewline <-
data.frame(findOverlaps(DisjoinSpanRange, NewLines.IR.ToHandle))
}
# mcols(DisjoinSpanRange)$Start.Prefix <- paste( "<span class=\"", mcols(DisjoinSpanRange)$Class,
# "\" title=\"", mcols(DisjoinSpanRange)$Title, "\">", sep = "")
GenomicRanges::mcols(DisjoinSpanRange)$Start.Prefix <-
paste(
"<span class=\"",
GenomicRanges::mcols(DisjoinSpanRange)$Class,
"\" data-toggle=\"popover\" data-html=\"true\" data-trigger=\"hover click\" data-placement=\"bottom\" title=\"Features\" data-content=\"",
GenomicRanges::mcols(DisjoinSpanRange)$Title,
"\">",
sep = ""
)
GenomicRanges::mcols(DisjoinSpanRange)$Start.Suffix <- ""
GenomicRanges::mcols(DisjoinSpanRange)$End.Prefix <- ""
GenomicRanges::mcols(DisjoinSpanRange)$End.Suffix <- "</span>"
LocalProteinSequence <-
UpdateSequence(BlocksPosition.IR, LocalProteinSequence)
LocalProteinSequence <-
UpdateSequence(DisjoinSpanRange, LocalProteinSequence)
LocalProteinSequence <-
UpdateSequence(NewLines.IR, LocalProteinSequence)
LocalProteinSequence <-
UpdateSequence(Protein.IR, LocalProteinSequence)
LocalProteinSequence <- paste(LocalProteinSequence, collapse = "")
return(LocalProteinSequence)
}
#' HTML_PrettyBlastSequence prepare and HTML ready string with some more informations
#'
#' @param Sequence String of the protein AA Sequence
#' @param Peptides data.frame of the peptides attributed to this protein
#' @param Rescue Not Used for now
#' @param LineWidth Number of AA before a new line (will not include the space inside)
#'
#' @return HTML string of the sequence embedded with features included as span
#' @import IRanges
#' @import GenomicRanges
#' @export
#'
#' @examples
#' library(Biostrings)
#' PB_FilePath <- system.file("extdata",
#' "protein_bank.example.fasta",
#' package = "isoformnspectRe")
#' ProteinBank<-readAAStringSet(
#' PB_FilePath
#' )
#' Sequence <- as.vector(ProteinBank["Example"])
#' Peptides <- data.frame(
#' Start = c(2, 2, 240),
#' End = c(10, 11, 253),
#' Pep = c(1.9437e-06, 0.00014334, 0.0001654),
#' Proteins = c(
#' "strngt.11487.1 Q8WUM4-3 strngt.11487.3 strngt.11487.2",
#' "strngt.11487.1 Q8WUM4-3 strngt.11487.3 strngt.11487.2",
#' "strngt.11487.2"),
#' Sequence = c("ATFISVQLK", "ATFISVQLKK", "YFYFQEVFPVLAAK ")
#' )
#' Sequence <- HTML_Pretty_Sequence(Sequence,Peptides)
HTML_PrettyBlastSequence<-function(
Sequence,
Peptides,
Rescue,
LineWidth=60){
#Protein IntegerRange
LocalProteinSequence <- unlist(strsplit(x = as.vector(Sequence), split = ""))
LocalProteinLength<-length(LocalProteinSequence)
Protein.IR <- IRanges(start = 1, end = LocalProteinLength)
mcols(Protein.IR) <- data.frame(
Class = "Protein",
Start.Prefix = "<div style=\"font-family:monospace;font-size:16px;height:100%;overflow-y:scroll;\">",
Start.Suffix = "",
End.Prefix = "",
End.Suffix = paste(
HTML_HandleEndOfLine(LocalProteinLength, LineWidth),
"</div>"
)
)
#Newline IntegerRange
if(LocalProteinLength>LineWidth){
NewLines<-seq(LineWidth,LocalProteinLength,LineWidth)
NewLines<-NewLines[!NewLines %in% LocalProteinLength]
NewLines.AfterChar<-unlist( lapply( NewLines, function(x) HTML_HandleEndOfLine(x,LineWidth)))
NewLines.IR<-IRanges( start=NewLines, end=NewLines)
mcols(NewLines.IR)<-data.frame(Class="Newline", Start.Prefix="",
Start.Suffix="", End.Prefix="", End.Suffix=NewLines.AfterChar)
}else{
NewLines.IR<-IRanges()
NewLines<-c()
}
#Block IntegerRange
BlocksPosition<-seq(10, LocalProteinLength, 10)
BlocksPosition<-BlocksPosition[!BlocksPosition %in% NewLines]
BlocksPosition.IR <- IRanges(start = BlocksPosition, end = BlocksPosition)
mcols(BlocksPosition.IR) <- data.frame(
Class = "BlockEnd",
Start.Prefix = "",
Start.Suffix = "",
End.Prefix = "",
End.Suffix = " "
)
#Blast differences
Blast.IR <- IRanges(start = Rescue$QueryStart,
end = Rescue$QueryEnd)
mcols(Blast.IR) <- data.frame(
Class = "Blast",
Title = paste(
Rescue$SubjectSeqId,
" from:",
Rescue$SubjectStart,
" to:",
Rescue$SubjectEnd,
" of: ",
Rescue$SubjectLength,
sep = ""
)
)
Diffs.IR<-CompareTwoSequences(as.vector(Rescue$QuerySequence),
as.vector(Rescue$SubjectSequence),
Rescue$QueryStart)
Blast.IR<-c(Blast.IR, Diffs.IR)
IDX_Shared <- grep(" ",Peptides$Proteins)
IDX_Proteotypic <- grep(" ",Peptides$Proteins,invert = TRUE)
#ProteotypicIntergerRange
SharedPeptides.IR <- IRanges(start = Peptides$Start[IDX_Shared],
end = Peptides$End[IDX_Shared])
mcols(SharedPeptides.IR) <- data.frame(
Title = paste(
"Peptide: ",
Peptides$Sequence[IDX_Shared],
"(",
formatC(Peptides$Pep[IDX_Shared], digits = 2),
")\n",
sep = ""
),
Class = "Peptide"
)
#PeptidesIntergerRange
Proteotypic.IR <- IRanges(start = Peptides$Start[IDX_Proteotypic],
end = Peptides$End[IDX_Proteotypic])
mcols(Proteotypic.IR) <- data.frame(
Title = paste(
"Peptide: ",
Peptides$Sequence[IDX_Proteotypic],
"(",
formatC(Peptides$Pep[IDX_Proteotypic], digits = 2),
")\n",
sep = ""
),
Class = "Peptide Proteotypic"
)
Peptides.IR<-c(SharedPeptides.IR,Proteotypic.IR)
#Infos
SpanRanges<-c(Blast.IR,Peptides.IR)
SpanRanges<-CollapseSpanRanges(SpanRanges)
DisjoinSpanRange<-SplitSpanRanges(SpanRanges,NewLines.IR)
mcols(DisjoinSpanRange)$Start.Prefix <- paste("<span class=\"", mcols(DisjoinSpanRange)$Class, "\" title=\"",
mcols(DisjoinSpanRange)$Title, "\">", sep = "")
mcols(DisjoinSpanRange)$Start.Suffix <- ""
mcols(DisjoinSpanRange)$End.Prefix <- ""
mcols(DisjoinSpanRange)$End.Suffix <- "</span>"
#Insert Newlines into Disjoin IntegerRange
NewLines.IR.ToHandle<-NewLines.IR
OverlapsWithNewline<-data.frame(findOverlaps(DisjoinSpanRange,NewLines.IR.ToHandle))
while(dim(OverlapsWithNewline)[1]>0){
##Case where the a peptide end with a new line it created a span that did not close anywhere and in doing so make it all
if (end(DisjoinSpanRange[OverlapsWithNewline$queryHits[1]])==end(NewLines.IR.ToHandle[OverlapsWithNewline$subjectHits[1]])) {
} else{
Before <- DisjoinSpanRange[OverlapsWithNewline$queryHits[1]]
After <- Before
end(Before) <- start(NewLines.IR.ToHandle[OverlapsWithNewline$subjectHits[1]])
start(After) <- end(NewLines.IR.ToHandle[OverlapsWithNewline$subjectHits[1]]) + 1
DisjoinSpanRange <- DisjoinSpanRange[-OverlapsWithNewline$queryHits[1]]
DisjoinSpanRange <- c(DisjoinSpanRange, Before, After)
DisjoinSpanRange <- sort(DisjoinSpanRange)
}
NewLines.IR.ToHandle<-NewLines.IR.ToHandle[-OverlapsWithNewline$subjectHits[1]]
OverlapsWithNewline<-data.frame(findOverlaps(DisjoinSpanRange,NewLines.IR.ToHandle))
}
# mcols(DisjoinSpanRange)$Start.Prefix <- paste( "<span class=\"", mcols(DisjoinSpanRange)$Class,
# "\" title=\"", mcols(DisjoinSpanRange)$Title, "\">", sep = "")
mcols(DisjoinSpanRange)$Start.Prefix <- paste("<span class=\"", mcols(DisjoinSpanRange)$Class,
"\" data-toggle=\"popover\" data-html=\"true\" data-trigger=\"hover click\" data-placement=\"bottom\" title=\"Features\" data-content=\"", mcols(DisjoinSpanRange)$Title, "\">", sep = "")
mcols(DisjoinSpanRange)$Start.Suffix <- ""
mcols(DisjoinSpanRange)$End.Prefix <- ""
mcols(DisjoinSpanRange)$End.Suffix <- "</span>"
LocalProteinSequence<-UpdateSequence(BlocksPosition.IR, LocalProteinSequence)
LocalProteinSequence<-UpdateSequence(DisjoinSpanRange, LocalProteinSequence)
LocalProteinSequence<-UpdateSequence(NewLines.IR, LocalProteinSequence)
LocalProteinSequence<-UpdateSequence(Protein.IR, LocalProteinSequence)
LocalProteinSequence<-paste(LocalProteinSequence, collapse="")
#Status
PeptideInSAAV <- FALSE
PeptideInInsertion <- FALSE
PeptideInDeletion <- FALSE
PeptideOutOfBlastSAAV <- FALSE
SAAV <- FALSE
Insertion <- FALSE
Deletion <- FALSE
if(sum(mcols(Blast.IR)$Class=="SAAV")>0){SAAV <- TRUE}
if(sum(mcols(Blast.IR)$Class=="Insertion")>0){Insertion <- TRUE}
if(sum(mcols(Blast.IR)$Class=="Deletion")>0){Deletion <- TRUE}
if(sum(Peptides.IR %over% Blast.IR[mcols(Blast.IR)$Class=="SAAV"])>0){ PeptideInSAAV <- TRUE}
if(sum(Peptides.IR %over% Blast.IR[mcols(Blast.IR)$Class=="Insertion"])>0){ PeptideInInsertion <- TRUE}
if(sum(Peptides.IR %over% Blast.IR[mcols(Blast.IR)$Class=="Deletion"])>0){ PeptideInDeletion <- TRUE}
if(sum(!Peptides.IR %over% Blast.IR)>0){ PeptideOutOfBlastSAAV <- TRUE}
return(list(SequenceInHTML=LocalProteinSequence,
SAAVxPep=PeptideInSAAV,
SAAV=SAAV,
InsertionxPep=PeptideInInsertion,
Insertion=Insertion,
DeletionxPep=PeptideInDeletion,
Deletion=Deletion,
OutOfBlast=PeptideOutOfBlastSAAV))
}
#' Alter a peptide sequence to have an harmonious presentation
#'
#' @param Sequences Vector of peptides Sequence
#' @param MaxNChar Maximum width size of the peptide
#' @return string vector as a HTML span to have shorter form
#' @export
#'
#' @examples
#' library("DT")
#' library("data.table")
#' P_FilePath <- system.file("extdata",
#' "peptides.example.txt",
#' package = "isoformnspectRe")
#' Peptides<-fread(
#' P_FilePath,
#' integer64="double")
#' Peptides<-Peptides[,c("Sequence",
#' "Start position","End position")]
#' datatable(Peptides)
#' Peptides$Sequence<-HTML_VECTOR_Peptide2Popover(Peptides$Sequence)
#' datatable(Peptides,escape=FALSE,
#' options=list(
#' drawCallback=JS(
#' paste("$('[data-toggle=\"popover\"]').popover({container: 'body'});")
#' )))
HTML_VECTOR_Peptide2Popover<-function(Sequences,MaxNChar=15){
Too_Long_Sequence_Lengths <- nchar(Sequences) > 15
Sequences[Too_Long_Sequence_Lengths] <- paste(
"<span data-toggle=\"popover\"
data-trigger=\"hover click\" data-placement=\"right\"
data-html=\"true\" data-delay={show: 500, hide: 100}
title=\"Proteins\" data-content=\"",
Sequences[Too_Long_Sequence_Lengths],"\">",
base::substr(Sequences[Too_Long_Sequence_Lengths],
1,MaxNChar-3),
"...</span>",sep="")
return(Sequences)
}
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