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@darth-donut
darth-donut committed Oct 24, 2018
2 parents 03db7d0 + 03a0f4c commit a0e03f4
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6 changes: 4 additions & 2 deletions DESCRIPTION
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Expand Up @@ -15,7 +15,7 @@ License: GPL-3 | file LICENSE
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.5.0)
Imports:
Imports:
ggplot2,
RColorBrewer,
circlize,
Expand Down Expand Up @@ -43,7 +43,8 @@ Imports:
graphics
VignetteBuilder: knitr
RoxygenNote: 6.1.0
Collate:
Collate:
'accessors-AbSeq.R'
'AbSeqCRep.R'
'util.R'
'distributions.R'
Expand All @@ -66,3 +67,4 @@ biocViews: Sequencing,
ReportWriting,
QualityControl,
MultipleComparison
Suggests: testthat
2 changes: 1 addition & 1 deletion Makefile
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Expand Up @@ -21,7 +21,7 @@ vignette:
rm -rf vignettes/ex/ vignettes/refined_comparison/

clean:
rm -rf vignettes/ex/ vignettes/refined_comparison/ vignettes/abseqR.html
rm -f tests/testthat/Rplots.pdf vignettes/abseqR.html

help:
@echo -e "Available commands:"
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5 changes: 4 additions & 1 deletion R/AbSeqCRep.R
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Expand Up @@ -42,6 +42,8 @@ AbSeqCRep <-

#' Combines 2 \linkS4class{AbSeqCRep} objects together for comparison
#'
#' @include accessors-AbSeq.R
#'
#' @param e1 AbSeqCRep.
#' @param e2 AbSeqCRep.
#'
Expand Down Expand Up @@ -74,6 +76,7 @@ setMethod("+",
e2 = "AbSeqCRep"),
function(e1, e2) {
new("AbSeqCRep",
repertoires = unique(c(e1@repertoires, e2@repertoires)))
repertoires = unique(c(.asRepertoireList(e1),
.asRepertoireList(e2))))

})
140 changes: 66 additions & 74 deletions R/AbSeqRep.R
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Original file line number Diff line number Diff line change
Expand Up @@ -90,10 +90,6 @@
#' abseqPyOutput <- tempdir()
#' file.copy(system.file("extdata", "ex", package = "abseqR"), abseqPyOutput, recursive=TRUE)
#' samples <- abseqReport(file.path(abseqPyOutput, "ex"), report = 0)
#'
#'
#' # gives the name of the first repertoire object returned by abseqReport
#' # samples[[1]]@name
AbSeqRep <- setClass(
"AbSeqRep",
slots = c(
Expand Down Expand Up @@ -205,6 +201,7 @@ setMethod("+", signature(e1 = "AbSeqRep", e2 = "AbSeqRep"), function(e1, e2) {
#' a \linkS4class{AbSeqRep} object together for comparison
#'
#' @include AbSeqCRep.R
#' @include accessors-AbSeq.R
#'
#' @param e1 AbSeqCRep.
#' @param e2 AbSeqRep.
Expand Down Expand Up @@ -235,13 +232,14 @@ setMethod("+", signature(e1 = "AbSeqRep", e2 = "AbSeqRep"), function(e1, e2) {
#' # you can now call the report function on this object
#' # report(pcr123) # uncomment this line to execute report
setMethod("+", signature(e1 = "AbSeqCRep", e2 = "AbSeqRep"), function(e1, e2) {
new("AbSeqCRep", repertoires = unique(c(e1@repertoires, e2)))
new("AbSeqCRep", repertoires = unique(c(.asRepertoireList(e1), e2)))
})

#' Combines a \linkS4class{AbSeqRep} object with
#' a \linkS4class{AbSeqCRep} object together for comparison
#'
#' @include AbSeqCRep.R
#' @include accessors-AbSeq.R
#'
#' @param e1 AbSeqRep.
#' @param e2 AbSeqCRep.
Expand Down Expand Up @@ -272,7 +270,7 @@ setMethod("+", signature(e1 = "AbSeqCRep", e2 = "AbSeqRep"), function(e1, e2) {
#' # you can now call the report function on this object
#' # report(pcr123) # uncomment this line to execute report
setMethod("+", signature(e1 = "AbSeqRep", e2 = "AbSeqCRep"), function(e1, e2) {
new("AbSeqCRep", repertoires = unique(c(e1, e2@repertoires)))
new("AbSeqCRep", repertoires = unique(c(e1, .asRepertoireList(e2))))
})

#' Plots \linkS4class{AbSeqRep} or
Expand All @@ -294,6 +292,7 @@ setMethod("+", signature(e1 = "AbSeqRep", e2 = "AbSeqCRep"), function(e1, e2) {
#'
#' @include util.R
#' @include plotter.R
#' @include accessors-AbSeq.R
#' @include AbSeqCRep.R
#'
#' @param object AbSeqRep or AbSeqCRep object to plot.
Expand Down Expand Up @@ -381,16 +380,17 @@ setMethod(
}

if (!skip) {
analysisDirectories = c(file.path(object@outdir,
RESULT_DIR, object@name))
analysisDirectories = c(file.path(.asRepertoireDir(object),
RESULT_DIR,
.asRepertoireName(object)))
# get analysis that were conducted by looking at the directory
# structure
analyses <-
unlist(.inferAnalyzed(analysisDirectories[1]))
sampleNames <- c(object@name)
primer5Files <- list(object@primer5end)
primer3Files <- list(object@primer3end)
upstreamRanges <- list(object@upstream)
sampleNames <- .asRepertoireName(object)
primer5Files <- list(.asRepertoirePrimer5(object))
primer3Files <- list(.asRepertoirePrimer3(object))
upstreamRanges <- list(.asRepertoireUpstream(object))

.plotSamples(
sampleNames,
Expand All @@ -400,7 +400,7 @@ setMethod(
primer5Files,
primer3Files,
upstreamRanges,
skipDgene = (object@chain != "hv")
skipDgene = (.asRepertoireChain(object) != "hv")
)

if (report) {
Expand All @@ -415,7 +415,7 @@ setMethod(

# to be consistent with the return value of abseqR::abseqReport()
lst <- list()
lst[[object@name]] <- object
lst[[.asRepertoireName(object)]] <- object
return(lst)
}
)
Expand Down Expand Up @@ -443,15 +443,18 @@ setMethod(
}

sampleNames <-
unlist(lapply(object@repertoires, function(x) {
x@name
}))
unlist(lapply(.asRepertoireList(object), .asRepertoireName))

if (!skip) {
analysisDirectories <- unlist(lapply(object@repertoires, function(x) {
# /a/b/c/RESULT_DIR/sample_name has all the analysis folders
file.path(x@outdir, RESULT_DIR, x@name)
}))
analysisDirectories <- unlist(
lapply(
.asRepertoireList(object), function(x) {
# /a/b/c/RESULT_DIR/sample_name has
# all the analysis folders
file.path(.asRepertoireDir(x),
RESULT_DIR,
.asRepertoireName(x))
}))

# get all analyses conducted by each repertoire by looking
# at the directory structure created by abseqPy
Expand All @@ -463,23 +466,16 @@ setMethod(


primer5Files <-
unlist(lapply(object@repertoires, function(x) {
x@primer5end
}))
unlist(lapply(.asRepertoireList(object), .asRepertoirePrimer5))

primer3Files <-
unlist(lapply(object@repertoires, function(x) {
x@primer3end
}))
unlist(lapply(.asRepertoireList(object), .asRepertoirePrimer3))

upstreamRanges <- lapply(object@repertoires,
function(x) {
x@upstream
})
upstreamRanges <- lapply(.asRepertoireList(object),
.asRepertoireUpstream)

allChains <- lapply(.asRepertoireList(object), .asRepertoireChain)

allChains <-
lapply(object@repertoires, function(x) {
x@chain
})
# only include D gene plots if all chains only contain "hv"
skipD <- (("kv" %in% allChains) || ("lv" %in% allChains))

Expand All @@ -504,7 +500,7 @@ setMethod(
}
}

lst <- object@repertoires
lst <- .asRepertoireList(object)
names(lst) <- sampleNames
return(lst)
}
Expand All @@ -516,6 +512,7 @@ setMethod(
#'
#' @importFrom rmarkdown pandoc_available render
#' @include util.R
#' @include accessors-AbSeq.R
#'
#' @param object AbSeqCRep type.
#' @param root string type. Root directory of the sample(s)
Expand Down Expand Up @@ -545,18 +542,18 @@ setMethod(
interactivePlot = TRUE,
.indexHTML = "#") {
if (rmarkdown::pandoc_available()) {
analysisDirectories = unlist(lapply(object@repertoires, function(x) {
# /a/b/c/RESULT_DIR/sample_name has all the analysis folders
file.path(x@outdir, RESULT_DIR, x@name)
}))
analysisDirectories = unlist(
lapply(
.asRepertoireList(object), function(x) {
# /a/b/c/RESULT_DIR/sample_name has all the analysis folders
file.path(.asRepertoireDir(x), RESULT_DIR, .asRepertoireName(x))
}))

sampleNames <-
unlist(lapply(object@repertoires, function(x) {
x@name
}))
message(paste(
"Generating HTML report for",
paste(sampleNames, collapse = "_vs_")
))
unlist(lapply(.asRepertoireList(object), .asRepertoireName))

message("Generating HTML report for ",
paste(sampleNames, collapse = "_vs_"))

# get all analyses conducted by each repertoire by looking
# at the directory structure created by abseqPy
Expand All @@ -568,30 +565,25 @@ setMethod(

# define variables for template.Rmd's param list
allChains <-
lapply(object@repertoires, function(x) {
x@chain
})
lapply(.asRepertoireList(object), .asRepertoireChain)

# only include D gene plots if all chains only contain "hv"
includeD <- !(("kv" %in% allChains) || ("lv" %in% allChains))


# template.Rmd param list
bitFilters <-
lapply(object@repertoires, function(x) {
paste(x@bitscore, collapse = " - ")
})
lapply(.asRepertoireList(object), .asRepertoireBitscore)

alFilters <-
lapply(object@repertoires, function(x) {
paste(x@alignlen, collapse = " - ")
})
lapply(.asRepertoireList(object), .asRepertoireAlignLen)

ssFilters <-
lapply(object@repertoires, function(x) {
paste(x@sstart, collapse = " - ")
})
lapply(.asRepertoireList(object), .asRepertoireSubjectStart)

qsFilters <-
lapply(object@repertoires, function(x) {
paste(x@qstart, collapse = " - ")
})
lapply(.asRepertoireList(object), .asRepertoireQueryStart)

rawReadCounts <- lapply(X = analysisDirectories,
FUN = .readSummary,
ABSEQ_RAW_READ_COUNT_KEY)
Expand Down Expand Up @@ -665,18 +657,18 @@ setMethod(
interactivePlot = TRUE,
.indexHTML = "#") {
if (rmarkdown::pandoc_available()) {
message(paste("Generating HTML report for", object@name))
analysisDirectory = file.path(object@outdir, RESULT_DIR, object@name)
message("Generating HTML report for ", .asRepertoireName(object))
analysisDirectory = file.path(.asRepertoireDir(object),
RESULT_DIR,
.asRepertoireName(object))
analyses <-
unlist(.inferAnalyzed(analysisDirectory))

# define parameters for template.Rmd's param list
bitFilter <-
paste(object@bitscore, collapse = " - ")
qsFilter <- paste(object@qstart, collapse = " - ")
ssFilter <- paste(object@sstart, collapse = " - ")
alFilter <-
paste(object@alignlen, collapse = " - ")
bitFilter <- .asRepertoireBitscore(object)
qsFilter <- .asRepertoireQueryStart(object)
ssFilter <- .asRepertoireSubjectStart(object)
alFilter <- .asRepertoireAlignLen(object)
rawReadCount <- .readSummary(analysisDirectory,
ABSEQ_RAW_READ_COUNT_KEY)
annotReadCount <- .readSummary(analysisDirectory,
Expand All @@ -692,12 +684,12 @@ setMethod(
rootDir = normalizePath(root),
single = TRUE,
interactive = interactivePlot,
inclD = (object@chain == "hv"),
inclD = (.asRepertoireChain(object) == "hv"),
hasAnnot = (ABSEQ_DIR_ANNOT %in% analyses),
hasAbun = (ABSEQ_DIR_ABUN %in% analyses),
hasProd = (ABSEQ_DIR_PROD %in% analyses),
hasDiv = (ABSEQ_DIR_DIV %in% analyses),
name = object@name,
name = .asRepertoireName(object),
bitfilters = bitFilter,
qstartfilters = qsFilter,
sstartfilters = ssFilter,
Expand All @@ -714,8 +706,8 @@ setMethod(
# as a safety measure, rename the template.Rmd file to
# sample name so that the cache will not clash with other
# samples it it wasn't cleared in time
tmpTemplate <-
file.path(outputDir, paste0(object@name, ".Rmd"))
tmpTemplate <- file.path(outputDir,
paste0(.asRepertoireName(object), ".Rmd"))
file.copy(
system.file("extdata", "template.Rmd", package = "abseqR"),
tmpTemplate,
Expand Down
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