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Improvement of variable names
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@michaelgruenstaeudl
michaelgruenstaeudl committed Feb 5, 2024
1 parent cd289d6 commit 96a2220
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Showing 7 changed files with 143 additions and 137 deletions.
80 changes: 41 additions & 39 deletions R/PACVr.R
View file
Original file line number Diff line number Diff line change
Expand Up @@ -16,10 +16,10 @@ PACVr.parseName <- function (gbkData) {
return(read.gbSampleName(gbkData))
}

PACVr.parseRegions <- function (gbkData, gbkDataDF) {
raw_regions <- ExtractAllRegions(gbkDataDF)
regions <- fillDataFrame(gbkData, raw_regions)
return(regions)
PACVr.parseQuadripRegions <- function (gbkData, gbkDataDF) {
raw_quadripRegions <- ParseQuadripartiteStructure(gbkDataDF)
quadripRegions <- fillDataFrame(gbkData, raw_quadripRegions)
return(quadripRegions)
}

PACVr.parseSource <- function(gbkDataDF) {
Expand All @@ -38,11 +38,11 @@ PACVr.calcCoverage <-
return(coverage)
}

PACVr.generateIRGeneData <- function(genes, regions,
PACVr.generateIRGeneData <- function(genes, quadripRegions,
syntenyLineType) {
# Parse GenBank file
if ("IRb" %in% regions[, 4] &&
"IRa" %in% regions[, 4]) {
if ("IRb" %in% quadripRegions[, 4] &&
"IRa" %in% quadripRegions[, 4]) {
linkData <- GenerateIRSynteny(genes, syntenyLineType)
return(linkData)
}
Expand All @@ -52,7 +52,7 @@ PACVr.generateIRGeneData <- function(genes, regions,
PACVr.verboseInformation <- function(gbkData,
bamFile,
genes,
regions,
quadripRegions,
IRCheck,
output) {
sampleName <- read.gbSampleName(gbkData)
Expand All @@ -74,15 +74,15 @@ PACVr.verboseInformation <- function(gbkData,
dir.create(tmpDir)
}
# Step 3. Write output
writeTables(regions, bamFile, genes, tmpDir, sampleName)
writeTables(quadripRegions, bamFile, genes, tmpDir, sampleName)
if (IRCheck) {
checkIREquality(gbkData, regions, tmpDir, sampleName)
checkIREquality(gbkData, quadripRegions, tmpDir, sampleName)
}
}

PACVr.visualizeWithRCircos <- function(gbkData,
genes,
regions,
quadripRegions,
coverage,
windowSize,
logScale,
Expand All @@ -97,7 +97,7 @@ PACVr.visualizeWithRCircos <- function(gbkData,
visualizeWithRCircos(
plotTitle,
genes,
regions,
quadripRegions,
coverage,
windowSize,
threshold,
Expand All @@ -123,22 +123,24 @@ PACVr.visualizeWithRCircos <- function(gbkData,
#' log-transformed before visualizing it
#' @param threshold a numeric value that specifies the threshold for plotting
#' coverage depth bars in red as opposed to the default black
#' @param regionsCheck a numeric value that specifies if region analysis of
#' genome should be performed, and if performed, the type of line for
#' visualizing gene synteny;
#' 0 = region analysis and no line, 1 = region analysis and ribbon lines,
#' 2 = region analysis and solid lines, otherwise = no analysis and no line
#' @param IRCheck a numeric value that specifies if tests
#' for IRs of input genome should be performed, and - if IRs are present -
#' which line type to be used for visualizing gene synteny between IRs;
#' 0 = IR presence test but no synteny visualization,
#' 1 = IR presence test and synteny visualization, with ribbon lines between IRs,
#' 2 = IR presence test and synteny visualization, with solid lines between IRs,
#' otherwise = neither IR presence test nor synteny visualization
#' @param relative a boolean that specifies whether the threshold is a relative
#' value of the average coverage instead of an absolute value
#' @param textSize a numeric value that specifies the relative font size of the
#' text element in the visualization
#' @param verbose a boolean, that when TRUE, generates additional files with
#' detailed genomic region information;
#' requires a `regionsCheck` value that will perform region analysis
#' requires a `IRCheck` value that will perform region analysis
#' @param output a character string that specifies the name of, and path to,
#' the output file
#' @return A file in pdf format containing a circular visualization of the
#' submitted plastid sample.
#' input plastid genome and its sequence reads.
#' As a function, returns 0 in case of visualization success.
#' @export
#' @examples
Expand All @@ -147,15 +149,15 @@ PACVr.visualizeWithRCircos <- function(gbkData,
#' bamFile <- system.file("extdata", "NC_045072/NC_045072_subsampled.bam", package="PACVr")
#' outFile <- paste(tempdir(), "/NC_045072__all_reads.pdf", sep="")
#' PACVr.complete(gbkFile=gbkFile, bamFile=bamFile, windowSize=250, logScale=FALSE,
#' threshold=0.5, regionsCheck=1, relative=TRUE, textSize=0.5,
#' threshold=0.5, IRCheck=1, relative=TRUE, textSize=0.5,
#' verbose=FALSE, output=outFile)
#' }
#' \dontrun{
#' gbkFile <- system.file("extdata", "MG936619/MG936619.gb", package="PACVr")
#' bamFile <- system.file("extdata", "MG936619/MG936619_subsampled.bam", package="PACVr")
#' outFile <- paste(tempdir(), "/MG936619_CoverageViz.pdf", sep="")
#' PACVr.complete(gbkFile=gbkFile, bamFile=bamFile, windowSize=50, logScale=FALSE,
#' threshold=0.5, regionsCheck=NA, relative=TRUE, textSize=0.5,
#' threshold=0.5, IRCheck=NA, relative=TRUE, textSize=0.5,
#' verbose=FALSE, output=outFile)
#' }

Expand All @@ -164,27 +166,27 @@ PACVr.complete <- function(gbkFile,
windowSize=250,
logScale=FALSE,
threshold=0.5,
regionsCheck=NA,
IRCheck=NA,
relative=TRUE,
textSize=0.5,
verbose=FALSE,
output=NA) {
######################################################################
gbkData <- PACVr.read.gb(gbkFile)
isRegionsCheck <- getIsRegionsCheck(regionsCheck)
gbkDataDF <- read.gb2DF(gbkData, isRegionsCheck)
isIRCheck <- getIsIRCheck(IRCheck)
gbkDataDF <- read.gb2DF(gbkData, isIRCheck)
if (is.null(gbkDataDF)) {
logger::log_error(paste("No usable data to perform specified analysis"))
return(NULL)
}

###################################
if (isRegionsCheck) {
if (isIRCheck) {
logger::log_info('Parsing the different genome regions')
regions <- PACVr.parseRegions(gbkData,
gbkDataDF)
quadripRegions <- PACVr.parseQuadripRegions(gbkData,
gbkDataDF)
} else {
regions <- PACVr.parseSource(gbkDataDF)
quadripRegions <- PACVr.parseQuadripRegions(gbkDataDF)
}

###################################
Expand All @@ -198,26 +200,26 @@ PACVr.complete <- function(gbkFile,

###################################
linkData <- NULL
IRCheck <- isSyntenyLineType(regionsCheck)
IRCheck <- isSyntenyLineType(IRCheck)
if (IRCheck) {
logger::log_info('Inferring the IR regions and the genes within the IRs')
linkData <- PACVr.generateIRGeneData(genes,
regions,
regionsCheck)
quadripRegions,
IRCheck)
}

###################################
if (isRegionsCheck && verbose) {
if (isIRCheck && verbose) {
logger::log_info('Generating statistical information on the sequencing coverage')
PACVr.verboseInformation(gbkData,
bamFile,
genes,
regions,
quadripRegions,
IRCheck,
output)
} else if (verbose) {
logger::log_warn(paste0('Verbose output requires `regionsCheck` in ',
'`', deparse(getRegionsCheckTypes()), '`'))
logger::log_warn(paste0('Verbose output requires `IRCheck` in ',
'`', deparse(getIRCheckTypes()), '`'))
}

###################################
Expand All @@ -227,14 +229,14 @@ PACVr.complete <- function(gbkFile,
PACVr.visualizeWithRCircos(
gbkData,
genes,
regions,
quadripRegions,
coverage,
windowSize,
threshold,
logScale,
relative,
linkData,
regionsCheck,
IRCheck,
textSize
)
dev.off()
Expand All @@ -244,14 +246,14 @@ PACVr.complete <- function(gbkFile,
PACVr.visualizeWithRCircos(
gbkData,
genes,
regions,
quadripRegions,
coverage,
windowSize,
threshold,
logScale,
relative,
linkData,
regionsCheck,
IRCheck,
textSize
)
dev.off()
Expand Down
12 changes: 6 additions & 6 deletions R/helpers.R
View file
Original file line number Diff line number Diff line change
Expand Up @@ -3,10 +3,10 @@
#email="m_gruenstaeudl@fhsu.edu"
#version="2024.02.01.1736"

read.gb2DF <- function(gbkData, regionsCheck) {
read.gb2DF <- function(gbkData, IRPresenceAndSyntenyCheck) {
fileDF <- data.frame()
for (sample in gbkData) {
sampleDF <- parseFeatures(sample$FEATURES, regionsCheck)
sampleDF <- parseFeatures(sample$FEATURES, IRPresenceAndSyntenyCheck)
if (!is.null(sampleDF)) {
fileDF <- dplyr::bind_rows(fileDF, sampleDF)
}
Expand All @@ -18,7 +18,7 @@ read.gb2DF <- function(gbkData, regionsCheck) {
return(fileDF)
}

parseFeatures <- function(features, regionsCheck) {
parseFeatures <- function(features, IRPresenceAndSyntenyCheck) {
sampleDF <- data.frame()
for (feature in features) {
feature <- parseFeature(feature)
Expand All @@ -27,7 +27,7 @@ parseFeatures <- function(features, regionsCheck) {
}
}
# check if can we can use the sample
subsetCols <- checkFeatureQualifiers(sampleDF, regionsCheck)
subsetCols <- checkFeatureQualifiers(sampleDF, IRPresenceAndSyntenyCheck)
if (is.null(subsetCols)) {
return(NULL)
}
Expand Down Expand Up @@ -372,9 +372,9 @@ validateColors <- function(colorsToValidate) {
}
}

checkFeatureQualifiers <- function(sampleDF, regionsCheck) {
checkFeatureQualifiers <- function(sampleDF, IRPresenceAndSyntenyCheck) {
subsetCols <- c("gene", "note", "type")
if (regionsCheck) {
if (IRPresenceAndSyntenyCheck) {
subsetCols <- c(subsetCols, "standard_name")
}
missingCols <- subsetCols[!(subsetCols %in% colnames(sampleDF))]
Expand Down
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