Merge pull request #78 from DEploid-dev/use_deploid_utils

Use deploid utils

.Rbuildignore

@@ -58,6 +58,7 @@ src/DEploid/lasso/version
 ^tests/testthat/Rplots.pdf$
 ^tests/testthat/.*\.png$
 ^tests/testthat/.*\.html$
+codecov.yml
 
 # vignettes/
 ^vignettes/commbine.sh

.github/workflows/test-coverage.yaml

@@ -38,13 +38,10 @@ jobs:
           covr::to_cobertura(cov)
         shell: Rscript {0}
 
-      - uses: codecov/codecov-action@v4
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v5
         with:
-          fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
-          file: ./cobertura.xml
-          plugin: noop
-          disable_search: true
-          token: ${{ secrets.CODECOV_TOKEN }}
+          token: ${{ secrets.REPO_CODECOV_TOKEN }}
 
       - name: Show testthat output
         if: always()

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: DEploid
 Type: Package
 Title: Deconvolute Mixed Genomes with Unknown Proportions
-Version: 0.5.4
+Version: 0.5.5
 Authors@R: c(
     person("Joe", "Zhu", role=c("aut", "cre", "cph"), email="[email protected]"),
     person('Jacob', 'Almagro-Garcia', role=c('aut')),
@@ -26,7 +26,8 @@ URL: https://github.com/DEploid-dev/DEploid-r
 BugReports: https://github.com/DEploid-dev/DEploid-r/issues
 License: GPL (>= 3)
 Depends:
-    R (>= 3.1.0)
+    R (>= 3.1.0),
+    DEploid.utils (>= 0.0.1)
 Imports:
     Rcpp (>= 0.11.2),
     scales (>= 0.4.0),

NAMESPACE

@@ -16,6 +16,16 @@ export(plotObsExpWSAFPlotly)
 export(plotProportions)
 export(plotWSAFVsPLAFPlotly)
 export(plotWSAFvsPLAF)
+importFrom(DEploid.utils,computeObsWSAF)
+importFrom(DEploid.utils,extractCoverageFromTxt)
+importFrom(DEploid.utils,extractCoverageFromVcf)
+importFrom(DEploid.utils,extractPLAF)
+importFrom(DEploid.utils,haplotypePainter)
+importFrom(DEploid.utils,histWSAF)
+importFrom(DEploid.utils,plotAltVsRef)
+importFrom(DEploid.utils,plotObsExpWSAF)
+importFrom(DEploid.utils,plotProportions)
+importFrom(DEploid.utils,plotWSAFvsPLAF)
 importFrom(Rcpp,evalCpp)
 importFrom(grDevices,colorRampPalette)
 importFrom(grDevices,rainbow)

R/DEploid.utils.R

@@ -0,0 +1,315 @@
+#' @importFrom DEploid.utils extractCoverageFromTxt
+#' @title Extract read counts from plain text file
+#'
+#' @note The allele count files must be tab-delimited. The allele count files
+#'  contain three columns: chromosomes, positions and allele count.
+#'
+#' @param refFileName Path of the reference allele count file.
+#'
+#' @param altFileName Path of the alternative allele count file.
+#'
+#' @return A data.frame contains four columns: chromosomes, positions, reference
+#'  allele count, alternative allele count.
+#'
+#' @export
+#'
+#' @examples
+#' refFile <- system.file("extdata", "PG0390-C.test.ref", package = "DEploid")
+#' altFile <- system.file("extdata", "PG0390-C.test.alt", package = "DEploid")
+#' PG0390 <- extractCoverageFromTxt(refFile, altFile)
+#'
+DEploid.utils::extractCoverageFromTxt
+
+
+#' @importFrom DEploid.utils extractCoverageFromVcf
+#' @title Extract read counts from VCF
+#'
+#' @note The VCF file should only contain one sample. If more samples present in
+#'  the VCF, it only returns coverage for of the first sample.
+#'
+#' @param vcfFileName Path of the VCF file.
+#'
+#' @param ADFieldIndex Index of the AD field of the sample field. For example,
+#'  if the format is "GT:AD:DP:GQ:PL", the AD index is 2 (by default).
+#'
+#' @return A data.frame contains four columns: chromosomes, positions, reference
+#'  allele count, alternative allele count.
+#'
+#' @export
+#'
+#' @examples
+#' vcfFile <- system.file("extdata", "PG0390-C.test.vcf.gz", package = "DEploid")
+#' PG0390 <- extractCoverageFromVcf(vcfFile, "PG0390-C")
+#'
+DEploid.utils::extractCoverageFromVcf
+
+
+#' @importFrom DEploid.utils extractPLAF
+#'
+#' @title Extract PLAF
+#'
+#' @note The text file must have header, and population level allele frequency
+#'  recorded in the "PLAF" field.
+#'
+#' @param plafFileName Path of the PLAF text file.
+#'
+#' @return A numeric array of PLAF
+#'
+#' @export
+#'
+#' @examples
+#' plafFile <- system.file("extdata", "labStrains.test.PLAF.txt",
+#'   package = "DEploid"
+#' )
+#' plaf <- extractPLAF(plafFile)
+DEploid.utils::extractPLAF
+
+
+#' @importFrom DEploid.utils plotProportions
+#'
+#' @title Plot proportions
+#'
+#' @param proportions Matrix of the MCMC proportion samples. The matrix size is
+#'  number of the MCMC samples by the number of strains.
+#'
+#' @param title Figure title.
+#'
+#' @param cex.lab Label size.
+#'
+#' @param cex.main Title size.
+#'
+#' @param cex.axis Axis text size.
+#'
+#' @export
+#'
+#' @examples
+#' \dontrun{
+#' plafFile <- system.file("extdata", "labStrains.test.PLAF.txt",
+#'   package = "DEploid"
+#' )
+#' panelFile <- system.file("extdata", "labStrains.test.panel.txt",
+#'   package = "DEploid"
+#' )
+#' refFile <- system.file("extdata", "PG0390-C.test.ref", package = "DEploid")
+#' altFile <- system.file("extdata", "PG0390-C.test.alt", package = "DEploid")
+#' PG0390CoverageT <- extractCoverageFromTxt(refFile, altFile)
+#' PG0390Coverage.deconv <- dEploid(paste(
+#'   "-ref", refFile, "-alt", altFile,
+#'   "-plaf", plafFile, "-noPanel"
+#' ))
+#' plotProportions(PG0390Coverage.deconv$Proportions, "PG0390-C proportions")
+#' }
+#'
+DEploid.utils::plotProportions
+
+
+#' @importFrom DEploid.utils plotAltVsRef
+#'
+#' @title Plot coverage
+#'
+#' @param ref Numeric array of reference allele count.
+#'
+#' @param alt Numeric array of alternative allele count.
+#'
+#' @param title Figure title, "Alt vs Ref" by default
+#'
+#' @param exclude.ref Numeric array of reference allele count at sites that are
+#' not deconvoluted.
+#'
+#' @param exclude.alt Numeric array of alternative allele count at sites that
+#'  are not deconvoluted
+#'
+#' @param potentialOutliers Index of potential outliers.
+#'
+#' @param cex.lab Label size.
+#'
+#' @param cex.main Title size.
+#'
+#' @param cex.axis Axis text size.
+#'
+#' @export
+#'
+#' @examples
+#' # Example 1
+#' refFile <- system.file("extdata", "PG0390-C.test.ref", package = "DEploid")
+#' altFile <- system.file("extdata", "PG0390-C.test.alt", package = "DEploid")
+#' PG0390CoverageT <- extractCoverageFromTxt(refFile, altFile)
+#' plotAltVsRef(PG0390CoverageT$refCount, PG0390CoverageT$altCount)
+#'
+#' # Example 2
+#' vcfFile <- system.file("extdata", "PG0390-C.test.vcf.gz", package = "DEploid")
+#' PG0390CoverageV <- extractCoverageFromVcf(vcfFile, "PG0390-C")
+#' plotAltVsRef(PG0390CoverageV$refCount, PG0390CoverageV$altCount)
+#'
+DEploid.utils::plotAltVsRef
+
+
+#' @importFrom DEploid.utils histWSAF
+#'
+#' @title WSAF histogram
+#'
+#' @param obsWSAF Observed allele frequency within sample
+#'
+#' @param exclusive When TRUE 0 < WSAF < 1; otherwise 0 <= WSAF <= 1.
+#'
+#' @param title Histogram title
+#'
+#' @param cex.lab Label size.
+#'
+#' @param cex.main Title size.
+#'
+#' @param cex.axis Axis text size.
+#'
+#' @return histogram
+#'
+#' @export
+#'
+#' @examples
+#' # Example 1
+#' refFile <- system.file("extdata", "PG0390-C.test.ref", package = "DEploid")
+#' altFile <- system.file("extdata", "PG0390-C.test.alt", package = "DEploid")
+#' PG0390Coverage <- extractCoverageFromTxt(refFile, altFile)
+#' obsWSAF <- computeObsWSAF(PG0390Coverage$altCount, PG0390Coverage$refCount)
+#' histWSAF(obsWSAF)
+#' myhist <- histWSAF(obsWSAF, FALSE)
+#'
+#' # Example 2
+#' vcfFile <- system.file("extdata", "PG0390-C.test.vcf.gz", package = "DEploid")
+#' PG0390CoverageV <- extractCoverageFromVcf(vcfFile, "PG0390-C")
+#' obsWSAF <- computeObsWSAF(PG0390CoverageV$altCount, PG0390CoverageV$refCount)
+#' histWSAF(obsWSAF)
+#' myhist <- histWSAF(obsWSAF, FALSE)
+#'
+DEploid.utils::histWSAF
+
+
+#' @importFrom DEploid.utils plotWSAFvsPLAF
+#'
+#' @title Plot WSAF vs PLAF
+#'
+#' @param plaf Numeric array of population level allele frequency.
+#'
+#' @param obsWSAF Numeric array of observed altenative allele frequencies within
+#'  sample.
+#'
+#' @param expWSAF Numeric array of expected WSAF from model.
+#'
+#' @param title Figure title, "WSAF vs PLAF" by default
+#'
+#' @param potentialOutliers Index of potential outliers.
+#'
+#' @param cex.lab Label size.
+#'
+#' @param cex.main Title size.
+#'
+#' @param cex.axis Axis text size.
+#'
+#' @export
+#'
+#' @examples
+#' # Example 1
+#' refFile <- system.file("extdata", "PG0390-C.test.ref", package = "DEploid")
+#' altFile <- system.file("extdata", "PG0390-C.test.alt", package = "DEploid")
+#' PG0390CoverageT <- extractCoverageFromTxt(refFile, altFile)
+#' obsWSAF <- computeObsWSAF(PG0390CoverageT$altCount, PG0390CoverageT$refCount)
+#' plafFile <- system.file("extdata", "labStrains.test.PLAF.txt",
+#'   package = "DEploid"
+#' )
+#' plaf <- extractPLAF(plafFile)
+#' plotWSAFvsPLAF(plaf, obsWSAF)
+#'
+#' # Example 2
+#' vcfFile <- system.file("extdata", "PG0390-C.test.vcf.gz", package = "DEploid")
+#' PG0390CoverageV <- extractCoverageFromVcf(vcfFile, "PG0390-C")
+#' obsWSAF <- computeObsWSAF(PG0390CoverageV$altCount, PG0390CoverageV$refCount)
+#' plafFile <- system.file("extdata", "labStrains.test.PLAF.txt",
+#'   package = "DEploid"
+#' )
+#' plaf <- extractPLAF(plafFile)
+#' plotWSAFvsPLAF(plaf, obsWSAF)
+#'
+DEploid.utils::plotWSAFvsPLAF
+
+
+#' @importFrom DEploid.utils plotObsExpWSAF
+#'
+#' @title Plot WSAF
+#'
+#' @param obsWSAF Numeric array of observed WSAF.
+#'
+#' @param expWSAF Numeric array of expected WSAF.
+#'
+#' @param title Figure title.
+#'
+#' @param cex.lab Label size.
+#'
+#' @param cex.main Title size.
+#'
+#' @param cex.axis Axis text size.
+#'
+#' @export
+#'
+#' @examples
+#'
+#' vcfFile <- system.file("extdata", "PG0390-C.test.vcf.gz", package = "DEploid")
+#' PG0390CoverageV <- extractCoverageFromVcf(vcfFile, "PG0390-C")
+#' obsWSAF <- computeObsWSAF(PG0390CoverageV$altCount, PG0390CoverageV$refCount)
+#' plafFile <- system.file("extdata", "labStrains.test.PLAF.txt",
+#'   package = "DEploid"
+#' )
+#' PG0390.deconv <- dEploid(paste(
+#'   "-vcf", vcfFile,
+#'   "-plaf", plafFile, "-noPanel"
+#' ))
+#' prop <- PG0390.deconv$Proportions[dim(PG0390.deconv$Proportions)[1], ]
+#' expWSAF <- t(PG0390.deconv$Haps) %*% prop
+#' plotObsExpWSAF(obsWSAF, expWSAF)
+#'
+DEploid.utils::plotObsExpWSAF
+
+
+#' @importFrom DEploid.utils computeObsWSAF
+#'
+#' @title Compute observed WSAF
+#'
+#' @param ref Numeric array of reference allele count.
+#'
+#' @param alt Numeric array of alternative allele count.
+#'
+#' @return Numeric array of observed allele frequency within sample.
+#'
+#' @seealso \code{\link{histWSAF}} for histogram.
+#'
+#' @export
+#'
+#' @examples
+#' # Example 1
+#' refFile <- system.file("extdata", "PG0390-C.test.ref", package = "DEploid")
+#' altFile <- system.file("extdata", "PG0390-C.test.alt", package = "DEploid")
+#' PG0390CoverageT <- extractCoverageFromTxt(refFile, altFile)
+#' obsWSAF <- computeObsWSAF(PG0390CoverageT$altCount, PG0390CoverageT$refCount)
+#'
+#' # Example 2
+#' vcfFile <- system.file("extdata", "PG0390-C.test.vcf.gz", package = "DEploid")
+#' PG0390CoverageV <- extractCoverageFromVcf(vcfFile, "PG0390-C")
+#' obsWSAF <- computeObsWSAF(PG0390CoverageV$altCount, PG0390CoverageV$refCount)
+#'
+DEploid.utils::computeObsWSAF
+
+
+#' @importFrom DEploid.utils haplotypePainter
+#'
+#' @title Painting haplotype according the reference panel
+#'
+#' @param posteriorProbabilities Posterior probabilities matrix with the size of
+#'  number of loci by the number of reference strain.
+#'
+#' @param title Figure title.
+#'
+#' @param labelScaling Scaling parameter for plotting.
+#'
+#' @param numberOfInbreeding Number of inbreeding strains copying from.
+#'
+#' @export
+#'
+DEploid.utils::haplotypePainter