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udpate news, and turn off widget, close #47, pandoc is not available …
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…on r-patched-solaris-x86
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@shajoezhu
shajoezhu committed Aug 9, 2017
1 parent c3d5d74 commit 8788180
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1 change: 1 addition & 0 deletions NEWS.md
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,7 @@
- None

## Improvements
- Include MCMC steps as dEploid function output
- Use `plotly` for generating new figures, including plotAltVsRefPlotly, plotHistWSAFPlotly, plotWSAFVsPLAFPlotly and plotObsExpWSAFPlotly


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16 changes: 12 additions & 4 deletions tests/testthat/test-DEploid_tools.R
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Original file line number Diff line number Diff line change
Expand Up @@ -49,7 +49,9 @@ test_that("WSAF Related", {
dev.off()
expect_that(inherits(plotHistWSAFPlotly(obsWSAF), "plotly"), is_true())
p <- plotHistWSAFPlotly(obsWSAF)
htmlwidgets::saveWidget(p, file = "histWSAFPlotly.html")
if (htmlwidgets:::pandoc_available()){
htmlwidgets::saveWidget(p, file = "histWSAFPlotly.html")
}
expect_null(plotWSAFvsPLAF(plaf, obsWSAF))
png("WSAFvsPLAF.png")
plotWSAFvsPLAF(plaf, obsWSAF)
Expand All @@ -62,15 +64,19 @@ test_that("WSAF Related", {
p <- plotWSAFVsPLAFPlotly(plaf, obsWSAF,
PG0390CoverageVcf$refCount,
PG0390CoverageVcf$altCount)
htmlwidgets::saveWidget(p, file = "WSAFvsPLAFPlotly.html")
if (htmlwidgets:::pandoc_available()){
htmlwidgets::saveWidget(p, file = "WSAFvsPLAFPlotly.html")
}
expect_null(plotObsExpWSAF(obsWSAF, expWSAF))
png("ObsExpWSAF.png")
plotObsExpWSAF(obsWSAF, expWSAF)
dev.off()
expect_that(inherits(plotObsExpWSAFPlotly(obsWSAF, expWSAF),
"plotly"), is_true())
p <- plotObsExpWSAFPlotly(obsWSAF, expWSAF)
htmlwidgets::saveWidget(p, file = "ObsExpWSAFPlotly.html")
if (htmlwidgets:::pandoc_available()){
htmlwidgets::saveWidget(p, file = "ObsExpWSAFPlotly.html")
}
})


Expand All @@ -85,7 +91,9 @@ test_that("plotAltVsRef", {
"plotly"), is_true())
p <- plotAltVsRefPlotly(PG0390CoverageVcf$refCount,
PG0390CoverageVcf$altCount)
htmlwidgets::saveWidget(p, file = "plotAltVsRefPlotly.html")
if (htmlwidgets:::pandoc_available()){
htmlwidgets::saveWidget(p, file = "plotAltVsRefPlotly.html")
}
})


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3 comments on commit 8788180

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R/dEploidPlotly.R:26:1: style: Variable or function name should be snake_case.

​plotAltVsRefPlotly <- function(ref, alt, title = "Alt vs Ref"){
^~~~~~~~~~~~~~~~~~

R/dEploidPlotly.R:28:5: style: Variable or function name should be snake_case.

​    legendName <- "Ref/(Ref+Alt) Ratio"
    ^~~~~~~~~~

R/dEploidPlotly.R:93:1: style: Variable or function name should be snake_case.

​plotHistWSAFPlotly <- function(obsWSAF, exclusive = TRUE,
^~~~~~~~~~~~~~~~~~

R/dEploidPlotly.R:93:32: style: Variable or function name should be snake_case.

​plotHistWSAFPlotly <- function(obsWSAF, exclusive = TRUE,
                               ^~~~~~~

R/dEploidPlotly.R:95:3: style: Variable or function name should be snake_case.

​  tmpWSAFIndex <- 1:length(obsWSAF)
  ^~~~~~~~~~~~

R/dEploidPlotly.R:97:5: style: Variable or function name should be snake_case.

​    tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
    ^~~~~~~~~~~~

R/dEploidPlotly.R:97:27: style: Do not place spaces around code in parentheses or square brackets.

​    tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
                          ^

R/dEploidPlotly.R:97:29: style: Do not place spaces around code in parentheses or square brackets.

​    tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
                            ^

R/dEploidPlotly.R:159:1: style: Variable or function name should be snake_case.

​plotWSAFVsPLAFPlotly <- function(plaf, obsWSAF, ref, alt,
^~~~~~~~~~~~~~~~~~~~

R/dEploidPlotly.R:159:40: style: Variable or function name should be snake_case.

​plotWSAFVsPLAFPlotly <- function(plaf, obsWSAF, ref, alt,
                                       ^~~~~~~

R/dEploidPlotly.R:208:1: style: Variable or function name should be snake_case.

​plotObsExpWSAFPlotly <- function(obsWSAF, expWSAF,
^~~~~~~~~~~~~~~~~~~~

R/dEploidPlotly.R:208:34: style: Variable or function name should be snake_case.

​plotObsExpWSAFPlotly <- function(obsWSAF, expWSAF,
                                 ^~~~~~~

R/dEploidPlotly.R:208:43: style: Variable or function name should be snake_case.

​plotObsExpWSAFPlotly <- function(obsWSAF, expWSAF,
                                          ^~~~~~~

R/DEploidR.R:23:1: style: Variable or function name should be snake_case.

​extractCoverageFromTxt <- function(refFileName, altFileName){
^~~~~~~~~~~~~~~~~~~~~~

R/DEploidR.R:23:36: style: Variable or function name should be snake_case.

​extractCoverageFromTxt <- function(refFileName, altFileName){
                                   ^~~~~~~~~~~

R/DEploidR.R:23:49: style: Variable or function name should be snake_case.

​extractCoverageFromTxt <- function(refFileName, altFileName){
                                                ^~~~~~~~~~~

R/DEploidR.R:54:1: style: Variable or function name should be snake_case.

​extractCoverageFromVcf <- function(vcfFileName, ADFieldIndex = 2){
^~~~~~~~~~~~~~~~~~~~~~

R/DEploidR.R:54:36: style: Variable or function name should be snake_case.

​extractCoverageFromVcf <- function(vcfFileName, ADFieldIndex = 2){
                                   ^~~~~~~~~~~

R/DEploidR.R:54:49: style: Variable or function name should be snake_case.

​extractCoverageFromVcf <- function(vcfFileName, ADFieldIndex = 2){
                                                ^~~~~~~~~~~~

R/DEploidR.R:62:5: style: Variable or function name should be snake_case.

​    numberOfHeaderLines <- 0
    ^~~~~~~~~~~~~~~~~~~

R/DEploidR.R:66:13: style: Variable or function name should be snake_case.

​            numberOfHeaderLines <- numberOfHeaderLines + 1
            ^~~~~~~~~~~~~~~~~~~

R/DEploidR.R:78:5: style: Variable or function name should be snake_case.

​    sampleName <- names(vcf)[10]
    ^~~~~~~~~~

R/DEploidR.R:83:5: style: Variable or function name should be snake_case.

​    tmpCovStr <- unlist(lapply(field, `[[`, ADFieldIndex))
    ^~~~~~~~~

R/DEploidR.R:84:5: style: Variable or function name should be snake_case.

​    tmpCov <- strsplit(as.character(tmpCovStr), ",")
    ^~~~~~

R/DEploidR.R:86:5: style: Variable or function name should be snake_case.

​    refCount <- as.numeric(unlist(lapply(tmpCov, `[[`, 1)))
    ^~~~~~~~

R/DEploidR.R:87:5: style: Variable or function name should be snake_case.

​    altCount <- as.numeric(unlist(lapply(tmpCov, `[[`, 2)))
    ^~~~~~~~

R/DEploidR.R:114:1: style: Variable or function name should be snake_case.

​extractPLAF <- function(plafFileName){
^~~~~~~~~~~

R/DEploidR.R:114:25: style: Variable or function name should be snake_case.

​extractPLAF <- function(plafFileName){
                        ^~~~~~~~~~~~

R/DEploidR.R:151:1: style: Variable or function name should be snake_case.

​plotProportions <- function(proportions, title = "Components",
^~~~~~~~~~~~~~~

R/DEploidR.R:152:24: style: Variable or function name should be snake_case.

​                       cex.lab = 1, cex.main = 1, cex.axis = 1){
                       ^~~~~~~

R/DEploidR.R:152:37: style: Variable or function name should be snake_case.

​                       cex.lab = 1, cex.main = 1, cex.axis = 1){
                                    ^~~~~~~~

R/DEploidR.R:152:51: style: Variable or function name should be snake_case.

​                       cex.lab = 1, cex.main = 1, cex.axis = 1){
                                                  ^~~~~~~~

R/DEploidR.R:153:5: style: Variable or function name should be snake_case.

​    rainbowColorBin <- 16
    ^~~~~~~~~~~~~~~

R/DEploidR.R:200:1: style: Variable or function name should be snake_case.

​plotAltVsRef <- function(ref, alt, title = "Alt vs Ref",
^~~~~~~~~~~~

R/DEploidR.R:201:21: style: Variable or function name should be snake_case.

​                    exclude.ref = c(), exclude.alt = c(),
                    ^~~~~~~~~~~

R/DEploidR.R:201:40: style: Variable or function name should be snake_case.

​                    exclude.ref = c(), exclude.alt = c(),
                                       ^~~~~~~~~~~

R/DEploidR.R:202:21: style: Variable or function name should be snake_case.

​                    potentialOutliers = c(), cex.lab = 1, cex.main = 1,
                    ^~~~~~~~~~~~~~~~~

R/DEploidR.R:202:46: style: Variable or function name should be snake_case.

​                    potentialOutliers = c(), cex.lab = 1, cex.main = 1,
                                             ^~~~~~~

R/DEploidR.R:202:59: style: Variable or function name should be snake_case.

​                    potentialOutliers = c(), cex.lab = 1, cex.main = 1,
                                                          ^~~~~~~~

R/DEploidR.R:203:21: style: Variable or function name should be snake_case.

​                    cex.axis = 1){
                    ^~~~~~~~

R/DEploidR.R:207:5: style: Variable or function name should be snake_case.

​    tmpRange <- 1.1 * mean(max(alt), max(ref))
    ^~~~~~~~

R/DEploidR.R:266:1: style: Variable or function name should be snake_case.

​histWSAF <- function(obsWSAF, exclusive = TRUE,
^~~~~~~~

R/DEploidR.R:266:22: style: Variable or function name should be snake_case.

​histWSAF <- function(obsWSAF, exclusive = TRUE,
                     ^~~~~~~

R/DEploidR.R:268:17: style: Variable or function name should be snake_case.

​                cex.lab = 1, cex.main = 1, cex.axis = 1){
                ^~~~~~~

R/DEploidR.R:268:30: style: Variable or function name should be snake_case.

​                cex.lab = 1, cex.main = 1, cex.axis = 1){
                             ^~~~~~~~

R/DEploidR.R:268:44: style: Variable or function name should be snake_case.

​                cex.lab = 1, cex.main = 1, cex.axis = 1){
                                           ^~~~~~~~

R/DEploidR.R:269:5: style: Variable or function name should be snake_case.

​    tmpWSAFIndex <- 1:length(obsWSAF)
    ^~~~~~~~~~~~

R/DEploidR.R:271:9: style: Variable or function name should be snake_case.

​        tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
        ^~~~~~~~~~~~

R/DEploidR.R:271:31: style: Do not place spaces around code in parentheses or square brackets.

​        tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
                              ^

R/DEploidR.R:271:33: style: Do not place spaces around code in parentheses or square brackets.

​        tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
                                ^

R/DEploidR.R:323:1: style: Variable or function name should be snake_case.

​plotWSAFvsPLAF <- function(plaf, obsWSAF, expWSAF = c(),
^~~~~~~~~~~~~~

R/DEploidR.R:323:34: style: Variable or function name should be snake_case.

​plotWSAFvsPLAF <- function(plaf, obsWSAF, expWSAF = c(),
                                 ^~~~~~~

R/DEploidR.R:323:43: style: Variable or function name should be snake_case.

​plotWSAFvsPLAF <- function(plaf, obsWSAF, expWSAF = c(),
                                          ^~~~~~~

R/DEploidR.R:324:23: style: Variable or function name should be snake_case.

​                      potentialOutliers = c(), title = "WSAF vs PLAF",
                      ^~~~~~~~~~~~~~~~~

R/DEploidR.R:325:23: style: Variable or function name should be snake_case.

​                      cex.lab = 1, cex.main = 1, cex.axis = 1){
                      ^~~~~~~

R/DEploidR.R:325:36: style: Variable or function name should be snake_case.

​                      cex.lab = 1, cex.main = 1, cex.axis = 1){
                                   ^~~~~~~~

R/DEploidR.R:325:50: style: Variable or function name should be snake_case.

​                      cex.lab = 1, cex.main = 1, cex.axis = 1){
                                                 ^~~~~~~~

R/DEploidR.R:368:1: style: Lines should not be more than 80 characters.

​#' prop = PG0390CoverageV.deconv$Proportions[dim(PG0390CoverageV.deconv$Proportions)[1],]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DEploidR.R:373:1: style: Variable or function name should be snake_case.

​plotObsExpWSAF <- function(obsWSAF, expWSAF,
^~~~~~~~~~~~~~

R/DEploidR.R:373:28: style: Variable or function name should be snake_case.

​plotObsExpWSAF <- function(obsWSAF, expWSAF,
                           ^~~~~~~

R/DEploidR.R:373:37: style: Variable or function name should be snake_case.

​plotObsExpWSAF <- function(obsWSAF, expWSAF,
                                    ^~~~~~~

R/DEploidR.R:375:23: style: Variable or function name should be snake_case.

​                      cex.lab = 1, cex.main = 1, cex.axis = 1){
                      ^~~~~~~

R/DEploidR.R:375:36: style: Variable or function name should be snake_case.

​                      cex.lab = 1, cex.main = 1, cex.axis = 1){
                                   ^~~~~~~~

R/DEploidR.R:375:50: style: Variable or function name should be snake_case.

​                      cex.lab = 1, cex.main = 1, cex.axis = 1){
                                                 ^~~~~~~~

R/DEploidR.R:411:1: style: Variable or function name should be snake_case.

​computeObsWSAF <- function(alt, ref){
^~~~~~~~~~~~~~

R/DEploidR.R:432:1: style: Variable or function name should be snake_case.

​haplotypePainter <- function(posteriorProbabilities, title = "", labelScaling,
^~~~~~~~~~~~~~~~

R/DEploidR.R:432:30: style: Variable or function name should be snake_case.

​haplotypePainter <- function(posteriorProbabilities, title = "", labelScaling,
                             ^~~~~~~~~~~~~~~~~~~~~~

R/DEploidR.R:432:66: style: Variable or function name should be snake_case.

​haplotypePainter <- function(posteriorProbabilities, title = "", labelScaling,
                                                                 ^~~~~~~~~~~~

R/DEploidR.R:433:25: style: Variable or function name should be snake_case.

​                        numberOfInbreeding = 0){
                        ^~~~~~~~~~~~~~~~~~

R/DEploidR.R:434:5: style: Variable or function name should be snake_case.

​    rainbowColorBin <- 16
    ^~~~~~~~~~~~~~~

R/DEploidR.R:435:5: style: Variable or function name should be snake_case.

​    rainbowColors <- rainbow(rainbowColorBin)
    ^~~~~~~~~~~~~

R/DEploidR.R:437:9: style: Variable or function name should be snake_case.

​        panelSize <- dim(posteriorProbabilities)[2] - numberOfInbreeding
        ^~~~~~~~~

R/DEploidR.R:438:9: style: Variable or function name should be snake_case.

​        rainbowColors <- c(rep("#46a8e1", panelSize),
        ^~~~~~~~~~~~~

R/DEploidR.R:446:5: style: Variable or function name should be snake_case.

​    newXaxt <- round(seq(1, dim(posteriorProbabilities)[1], length.out = 6))
    ^~~~~~~

R/DEploidR.R:449:5: style: Variable or function name should be snake_case.

​    newYaxt <- seq(0, 1, length.out = 3)
    ^~~~~~~

tests/testthat/test-DEploid_tools.R:3:1: style: Variable or function name should be snake_case.

​vcfFileName <- system.file("extdata", "PG0390-C.test.vcf.gz",
^~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:5:1: style: Variable or function name should be snake_case.

​plafFileName <- system.file("extdata", "labStrains.test.PLAF.txt",
^~~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:7:1: style: Variable or function name should be snake_case.

​panelFileName <- system.file("extdata", "labStrains.test.panel.txt",
^~~~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:9:1: style: Variable or function name should be snake_case.

​refFileName <- system.file("extdata", "PG0390-C.test.ref", package = "DEploid")
^~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:10:1: style: Variable or function name should be snake_case.

​altFileName <- system.file("extdata", "PG0390-C.test.alt", package = "DEploid")
^~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:12:1: style: Variable or function name should be snake_case.

​PG0390CoverageVcf <- extractCoverageFromVcf(vcfFileName)
^~~~~~~~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:15:1: style: Variable or function name should be snake_case.

​PG0390Deconv <- dEploid(paste("-vcf", vcfFileName, "-plaf", plafFileName,
^~~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:18:1: style: Variable or function name should be snake_case.

​expWSAF <- t(PG0390Deconv$Haps) %*% prop
^~~~~~~

tests/testthat/test-DEploid_tools.R:21:5: style: Variable or function name should be snake_case.

​    PG0390CoverageTxt <- extractCoverageFromTxt(refFileName, altFileName)
    ^~~~~~~~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:44:5: style: Variable or function name should be snake_case.

​    obsWSAF <- computeObsWSAF(PG0390CoverageVcf$altCount,
    ^~~~~~~

tests/testthat/test-dEploid.R:3:1: style: Variable or function name should be snake_case.

​vcfFileName <- system.file("extdata", "PG0390-C.test.vcf.gz",
^~~~~~~~~~~

tests/testthat/test-dEploid.R:5:1: style: Variable or function name should be snake_case.

​plafFileName <- system.file("extdata", "labStrains.test.PLAF.txt",
^~~~~~~~~~~~

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R/dEploidPlotly.R:26:1: style: Variable or function name should be snake_case.

​plotAltVsRefPlotly <- function(ref, alt, title = "Alt vs Ref"){
^~~~~~~~~~~~~~~~~~

R/dEploidPlotly.R:28:5: style: Variable or function name should be snake_case.

​    legendName <- "Ref/(Ref+Alt) Ratio"
    ^~~~~~~~~~

R/dEploidPlotly.R:93:1: style: Variable or function name should be snake_case.

​plotHistWSAFPlotly <- function(obsWSAF, exclusive = TRUE,
^~~~~~~~~~~~~~~~~~

R/dEploidPlotly.R:93:32: style: Variable or function name should be snake_case.

​plotHistWSAFPlotly <- function(obsWSAF, exclusive = TRUE,
                               ^~~~~~~

R/dEploidPlotly.R:95:3: style: Variable or function name should be snake_case.

​  tmpWSAFIndex <- 1:length(obsWSAF)
  ^~~~~~~~~~~~

R/dEploidPlotly.R:97:5: style: Variable or function name should be snake_case.

​    tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
    ^~~~~~~~~~~~

R/dEploidPlotly.R:97:27: style: Do not place spaces around code in parentheses or square brackets.

​    tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
                          ^

R/dEploidPlotly.R:97:29: style: Do not place spaces around code in parentheses or square brackets.

​    tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
                            ^

R/dEploidPlotly.R:159:1: style: Variable or function name should be snake_case.

​plotWSAFVsPLAFPlotly <- function(plaf, obsWSAF, ref, alt,
^~~~~~~~~~~~~~~~~~~~

R/dEploidPlotly.R:159:40: style: Variable or function name should be snake_case.

​plotWSAFVsPLAFPlotly <- function(plaf, obsWSAF, ref, alt,
                                       ^~~~~~~

R/dEploidPlotly.R:208:1: style: Variable or function name should be snake_case.

​plotObsExpWSAFPlotly <- function(obsWSAF, expWSAF,
^~~~~~~~~~~~~~~~~~~~

R/dEploidPlotly.R:208:34: style: Variable or function name should be snake_case.

​plotObsExpWSAFPlotly <- function(obsWSAF, expWSAF,
                                 ^~~~~~~

R/dEploidPlotly.R:208:43: style: Variable or function name should be snake_case.

​plotObsExpWSAFPlotly <- function(obsWSAF, expWSAF,
                                          ^~~~~~~

R/DEploidR.R:23:1: style: Variable or function name should be snake_case.

​extractCoverageFromTxt <- function(refFileName, altFileName){
^~~~~~~~~~~~~~~~~~~~~~

R/DEploidR.R:23:36: style: Variable or function name should be snake_case.

​extractCoverageFromTxt <- function(refFileName, altFileName){
                                   ^~~~~~~~~~~

R/DEploidR.R:23:49: style: Variable or function name should be snake_case.

​extractCoverageFromTxt <- function(refFileName, altFileName){
                                                ^~~~~~~~~~~

R/DEploidR.R:54:1: style: Variable or function name should be snake_case.

​extractCoverageFromVcf <- function(vcfFileName, ADFieldIndex = 2){
^~~~~~~~~~~~~~~~~~~~~~

R/DEploidR.R:54:36: style: Variable or function name should be snake_case.

​extractCoverageFromVcf <- function(vcfFileName, ADFieldIndex = 2){
                                   ^~~~~~~~~~~

R/DEploidR.R:54:49: style: Variable or function name should be snake_case.

​extractCoverageFromVcf <- function(vcfFileName, ADFieldIndex = 2){
                                                ^~~~~~~~~~~~

R/DEploidR.R:62:5: style: Variable or function name should be snake_case.

​    numberOfHeaderLines <- 0
    ^~~~~~~~~~~~~~~~~~~

R/DEploidR.R:66:13: style: Variable or function name should be snake_case.

​            numberOfHeaderLines <- numberOfHeaderLines + 1
            ^~~~~~~~~~~~~~~~~~~

R/DEploidR.R:78:5: style: Variable or function name should be snake_case.

​    sampleName <- names(vcf)[10]
    ^~~~~~~~~~

R/DEploidR.R:83:5: style: Variable or function name should be snake_case.

​    tmpCovStr <- unlist(lapply(field, `[[`, ADFieldIndex))
    ^~~~~~~~~

R/DEploidR.R:84:5: style: Variable or function name should be snake_case.

​    tmpCov <- strsplit(as.character(tmpCovStr), ",")
    ^~~~~~

R/DEploidR.R:86:5: style: Variable or function name should be snake_case.

​    refCount <- as.numeric(unlist(lapply(tmpCov, `[[`, 1)))
    ^~~~~~~~

R/DEploidR.R:87:5: style: Variable or function name should be snake_case.

​    altCount <- as.numeric(unlist(lapply(tmpCov, `[[`, 2)))
    ^~~~~~~~

R/DEploidR.R:114:1: style: Variable or function name should be snake_case.

​extractPLAF <- function(plafFileName){
^~~~~~~~~~~

R/DEploidR.R:114:25: style: Variable or function name should be snake_case.

​extractPLAF <- function(plafFileName){
                        ^~~~~~~~~~~~

R/DEploidR.R:151:1: style: Variable or function name should be snake_case.

​plotProportions <- function(proportions, title = "Components",
^~~~~~~~~~~~~~~

R/DEploidR.R:152:24: style: Variable or function name should be snake_case.

​                       cex.lab = 1, cex.main = 1, cex.axis = 1){
                       ^~~~~~~

R/DEploidR.R:152:37: style: Variable or function name should be snake_case.

​                       cex.lab = 1, cex.main = 1, cex.axis = 1){
                                    ^~~~~~~~

R/DEploidR.R:152:51: style: Variable or function name should be snake_case.

​                       cex.lab = 1, cex.main = 1, cex.axis = 1){
                                                  ^~~~~~~~

R/DEploidR.R:153:5: style: Variable or function name should be snake_case.

​    rainbowColorBin <- 16
    ^~~~~~~~~~~~~~~

R/DEploidR.R:200:1: style: Variable or function name should be snake_case.

​plotAltVsRef <- function(ref, alt, title = "Alt vs Ref",
^~~~~~~~~~~~

R/DEploidR.R:201:21: style: Variable or function name should be snake_case.

​                    exclude.ref = c(), exclude.alt = c(),
                    ^~~~~~~~~~~

R/DEploidR.R:201:40: style: Variable or function name should be snake_case.

​                    exclude.ref = c(), exclude.alt = c(),
                                       ^~~~~~~~~~~

R/DEploidR.R:202:21: style: Variable or function name should be snake_case.

​                    potentialOutliers = c(), cex.lab = 1, cex.main = 1,
                    ^~~~~~~~~~~~~~~~~

R/DEploidR.R:202:46: style: Variable or function name should be snake_case.

​                    potentialOutliers = c(), cex.lab = 1, cex.main = 1,
                                             ^~~~~~~

R/DEploidR.R:202:59: style: Variable or function name should be snake_case.

​                    potentialOutliers = c(), cex.lab = 1, cex.main = 1,
                                                          ^~~~~~~~

R/DEploidR.R:203:21: style: Variable or function name should be snake_case.

​                    cex.axis = 1){
                    ^~~~~~~~

R/DEploidR.R:207:5: style: Variable or function name should be snake_case.

​    tmpRange <- 1.1 * mean(max(alt), max(ref))
    ^~~~~~~~

R/DEploidR.R:266:1: style: Variable or function name should be snake_case.

​histWSAF <- function(obsWSAF, exclusive = TRUE,
^~~~~~~~

R/DEploidR.R:266:22: style: Variable or function name should be snake_case.

​histWSAF <- function(obsWSAF, exclusive = TRUE,
                     ^~~~~~~

R/DEploidR.R:268:17: style: Variable or function name should be snake_case.

​                cex.lab = 1, cex.main = 1, cex.axis = 1){
                ^~~~~~~

R/DEploidR.R:268:30: style: Variable or function name should be snake_case.

​                cex.lab = 1, cex.main = 1, cex.axis = 1){
                             ^~~~~~~~

R/DEploidR.R:268:44: style: Variable or function name should be snake_case.

​                cex.lab = 1, cex.main = 1, cex.axis = 1){
                                           ^~~~~~~~

R/DEploidR.R:269:5: style: Variable or function name should be snake_case.

​    tmpWSAFIndex <- 1:length(obsWSAF)
    ^~~~~~~~~~~~

R/DEploidR.R:271:9: style: Variable or function name should be snake_case.

​        tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
        ^~~~~~~~~~~~

R/DEploidR.R:271:31: style: Do not place spaces around code in parentheses or square brackets.

​        tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
                              ^

R/DEploidR.R:271:33: style: Do not place spaces around code in parentheses or square brackets.

​        tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
                                ^

R/DEploidR.R:323:1: style: Variable or function name should be snake_case.

​plotWSAFvsPLAF <- function(plaf, obsWSAF, expWSAF = c(),
^~~~~~~~~~~~~~

R/DEploidR.R:323:34: style: Variable or function name should be snake_case.

​plotWSAFvsPLAF <- function(plaf, obsWSAF, expWSAF = c(),
                                 ^~~~~~~

R/DEploidR.R:323:43: style: Variable or function name should be snake_case.

​plotWSAFvsPLAF <- function(plaf, obsWSAF, expWSAF = c(),
                                          ^~~~~~~

R/DEploidR.R:324:23: style: Variable or function name should be snake_case.

​                      potentialOutliers = c(), title = "WSAF vs PLAF",
                      ^~~~~~~~~~~~~~~~~

R/DEploidR.R:325:23: style: Variable or function name should be snake_case.

​                      cex.lab = 1, cex.main = 1, cex.axis = 1){
                      ^~~~~~~

R/DEploidR.R:325:36: style: Variable or function name should be snake_case.

​                      cex.lab = 1, cex.main = 1, cex.axis = 1){
                                   ^~~~~~~~

R/DEploidR.R:325:50: style: Variable or function name should be snake_case.

​                      cex.lab = 1, cex.main = 1, cex.axis = 1){
                                                 ^~~~~~~~

R/DEploidR.R:368:1: style: Lines should not be more than 80 characters.

​#' prop = PG0390CoverageV.deconv$Proportions[dim(PG0390CoverageV.deconv$Proportions)[1],]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DEploidR.R:373:1: style: Variable or function name should be snake_case.

​plotObsExpWSAF <- function(obsWSAF, expWSAF,
^~~~~~~~~~~~~~

R/DEploidR.R:373:28: style: Variable or function name should be snake_case.

​plotObsExpWSAF <- function(obsWSAF, expWSAF,
                           ^~~~~~~

R/DEploidR.R:373:37: style: Variable or function name should be snake_case.

​plotObsExpWSAF <- function(obsWSAF, expWSAF,
                                    ^~~~~~~

R/DEploidR.R:375:23: style: Variable or function name should be snake_case.

​                      cex.lab = 1, cex.main = 1, cex.axis = 1){
                      ^~~~~~~

R/DEploidR.R:375:36: style: Variable or function name should be snake_case.

​                      cex.lab = 1, cex.main = 1, cex.axis = 1){
                                   ^~~~~~~~

R/DEploidR.R:375:50: style: Variable or function name should be snake_case.

​                      cex.lab = 1, cex.main = 1, cex.axis = 1){
                                                 ^~~~~~~~

R/DEploidR.R:411:1: style: Variable or function name should be snake_case.

​computeObsWSAF <- function(alt, ref){
^~~~~~~~~~~~~~

R/DEploidR.R:432:1: style: Variable or function name should be snake_case.

​haplotypePainter <- function(posteriorProbabilities, title = "", labelScaling,
^~~~~~~~~~~~~~~~

R/DEploidR.R:432:30: style: Variable or function name should be snake_case.

​haplotypePainter <- function(posteriorProbabilities, title = "", labelScaling,
                             ^~~~~~~~~~~~~~~~~~~~~~

R/DEploidR.R:432:66: style: Variable or function name should be snake_case.

​haplotypePainter <- function(posteriorProbabilities, title = "", labelScaling,
                                                                 ^~~~~~~~~~~~

R/DEploidR.R:433:25: style: Variable or function name should be snake_case.

​                        numberOfInbreeding = 0){
                        ^~~~~~~~~~~~~~~~~~

R/DEploidR.R:434:5: style: Variable or function name should be snake_case.

​    rainbowColorBin <- 16
    ^~~~~~~~~~~~~~~

R/DEploidR.R:435:5: style: Variable or function name should be snake_case.

​    rainbowColors <- rainbow(rainbowColorBin)
    ^~~~~~~~~~~~~

R/DEploidR.R:437:9: style: Variable or function name should be snake_case.

​        panelSize <- dim(posteriorProbabilities)[2] - numberOfInbreeding
        ^~~~~~~~~

R/DEploidR.R:438:9: style: Variable or function name should be snake_case.

​        rainbowColors <- c(rep("#46a8e1", panelSize),
        ^~~~~~~~~~~~~

R/DEploidR.R:446:5: style: Variable or function name should be snake_case.

​    newXaxt <- round(seq(1, dim(posteriorProbabilities)[1], length.out = 6))
    ^~~~~~~

R/DEploidR.R:449:5: style: Variable or function name should be snake_case.

​    newYaxt <- seq(0, 1, length.out = 3)
    ^~~~~~~

tests/testthat/test-DEploid_tools.R:3:1: style: Variable or function name should be snake_case.

​vcfFileName <- system.file("extdata", "PG0390-C.test.vcf.gz",
^~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:5:1: style: Variable or function name should be snake_case.

​plafFileName <- system.file("extdata", "labStrains.test.PLAF.txt",
^~~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:7:1: style: Variable or function name should be snake_case.

​panelFileName <- system.file("extdata", "labStrains.test.panel.txt",
^~~~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:9:1: style: Variable or function name should be snake_case.

​refFileName <- system.file("extdata", "PG0390-C.test.ref", package = "DEploid")
^~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:10:1: style: Variable or function name should be snake_case.

​altFileName <- system.file("extdata", "PG0390-C.test.alt", package = "DEploid")
^~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:12:1: style: Variable or function name should be snake_case.

​PG0390CoverageVcf <- extractCoverageFromVcf(vcfFileName)
^~~~~~~~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:15:1: style: Variable or function name should be snake_case.

​PG0390Deconv <- dEploid(paste("-vcf", vcfFileName, "-plaf", plafFileName,
^~~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:18:1: style: Variable or function name should be snake_case.

​expWSAF <- t(PG0390Deconv$Haps) %*% prop
^~~~~~~

tests/testthat/test-DEploid_tools.R:21:5: style: Variable or function name should be snake_case.

​    PG0390CoverageTxt <- extractCoverageFromTxt(refFileName, altFileName)
    ^~~~~~~~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:44:5: style: Variable or function name should be snake_case.

​    obsWSAF <- computeObsWSAF(PG0390CoverageVcf$altCount,
    ^~~~~~~

tests/testthat/test-dEploid.R:3:1: style: Variable or function name should be snake_case.

​vcfFileName <- system.file("extdata", "PG0390-C.test.vcf.gz",
^~~~~~~~~~~

tests/testthat/test-dEploid.R:5:1: style: Variable or function name should be snake_case.

​plafFileName <- system.file("extdata", "labStrains.test.PLAF.txt",
^~~~~~~~~~~~

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R/dEploidPlotly.R:26:1: style: Variable or function name should be snake_case.

​plotAltVsRefPlotly <- function(ref, alt, title = "Alt vs Ref"){
^~~~~~~~~~~~~~~~~~

R/dEploidPlotly.R:28:5: style: Variable or function name should be snake_case.

​    legendName <- "Ref/(Ref+Alt) Ratio"
    ^~~~~~~~~~

R/dEploidPlotly.R:93:1: style: Variable or function name should be snake_case.

​plotHistWSAFPlotly <- function(obsWSAF, exclusive = TRUE,
^~~~~~~~~~~~~~~~~~

R/dEploidPlotly.R:93:32: style: Variable or function name should be snake_case.

​plotHistWSAFPlotly <- function(obsWSAF, exclusive = TRUE,
                               ^~~~~~~

R/dEploidPlotly.R:95:3: style: Variable or function name should be snake_case.

​  tmpWSAFIndex <- 1:length(obsWSAF)
  ^~~~~~~~~~~~

R/dEploidPlotly.R:97:5: style: Variable or function name should be snake_case.

​    tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
    ^~~~~~~~~~~~

R/dEploidPlotly.R:97:27: style: Do not place spaces around code in parentheses or square brackets.

​    tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
                          ^

R/dEploidPlotly.R:97:29: style: Do not place spaces around code in parentheses or square brackets.

​    tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
                            ^

R/dEploidPlotly.R:159:1: style: Variable or function name should be snake_case.

​plotWSAFVsPLAFPlotly <- function(plaf, obsWSAF, ref, alt,
^~~~~~~~~~~~~~~~~~~~

R/dEploidPlotly.R:159:40: style: Variable or function name should be snake_case.

​plotWSAFVsPLAFPlotly <- function(plaf, obsWSAF, ref, alt,
                                       ^~~~~~~

R/dEploidPlotly.R:208:1: style: Variable or function name should be snake_case.

​plotObsExpWSAFPlotly <- function(obsWSAF, expWSAF,
^~~~~~~~~~~~~~~~~~~~

R/dEploidPlotly.R:208:34: style: Variable or function name should be snake_case.

​plotObsExpWSAFPlotly <- function(obsWSAF, expWSAF,
                                 ^~~~~~~

R/dEploidPlotly.R:208:43: style: Variable or function name should be snake_case.

​plotObsExpWSAFPlotly <- function(obsWSAF, expWSAF,
                                          ^~~~~~~

R/DEploidR.R:23:1: style: Variable or function name should be snake_case.

​extractCoverageFromTxt <- function(refFileName, altFileName){
^~~~~~~~~~~~~~~~~~~~~~

R/DEploidR.R:23:36: style: Variable or function name should be snake_case.

​extractCoverageFromTxt <- function(refFileName, altFileName){
                                   ^~~~~~~~~~~

R/DEploidR.R:23:49: style: Variable or function name should be snake_case.

​extractCoverageFromTxt <- function(refFileName, altFileName){
                                                ^~~~~~~~~~~

R/DEploidR.R:54:1: style: Variable or function name should be snake_case.

​extractCoverageFromVcf <- function(vcfFileName, ADFieldIndex = 2){
^~~~~~~~~~~~~~~~~~~~~~

R/DEploidR.R:54:36: style: Variable or function name should be snake_case.

​extractCoverageFromVcf <- function(vcfFileName, ADFieldIndex = 2){
                                   ^~~~~~~~~~~

R/DEploidR.R:54:49: style: Variable or function name should be snake_case.

​extractCoverageFromVcf <- function(vcfFileName, ADFieldIndex = 2){
                                                ^~~~~~~~~~~~

R/DEploidR.R:62:5: style: Variable or function name should be snake_case.

​    numberOfHeaderLines <- 0
    ^~~~~~~~~~~~~~~~~~~

R/DEploidR.R:66:13: style: Variable or function name should be snake_case.

​            numberOfHeaderLines <- numberOfHeaderLines + 1
            ^~~~~~~~~~~~~~~~~~~

R/DEploidR.R:78:5: style: Variable or function name should be snake_case.

​    sampleName <- names(vcf)[10]
    ^~~~~~~~~~

R/DEploidR.R:83:5: style: Variable or function name should be snake_case.

​    tmpCovStr <- unlist(lapply(field, `[[`, ADFieldIndex))
    ^~~~~~~~~

R/DEploidR.R:84:5: style: Variable or function name should be snake_case.

​    tmpCov <- strsplit(as.character(tmpCovStr), ",")
    ^~~~~~

R/DEploidR.R:86:5: style: Variable or function name should be snake_case.

​    refCount <- as.numeric(unlist(lapply(tmpCov, `[[`, 1)))
    ^~~~~~~~

R/DEploidR.R:87:5: style: Variable or function name should be snake_case.

​    altCount <- as.numeric(unlist(lapply(tmpCov, `[[`, 2)))
    ^~~~~~~~

R/DEploidR.R:114:1: style: Variable or function name should be snake_case.

​extractPLAF <- function(plafFileName){
^~~~~~~~~~~

R/DEploidR.R:114:25: style: Variable or function name should be snake_case.

​extractPLAF <- function(plafFileName){
                        ^~~~~~~~~~~~

R/DEploidR.R:151:1: style: Variable or function name should be snake_case.

​plotProportions <- function(proportions, title = "Components",
^~~~~~~~~~~~~~~

R/DEploidR.R:152:24: style: Variable or function name should be snake_case.

​                       cex.lab = 1, cex.main = 1, cex.axis = 1){
                       ^~~~~~~

R/DEploidR.R:152:37: style: Variable or function name should be snake_case.

​                       cex.lab = 1, cex.main = 1, cex.axis = 1){
                                    ^~~~~~~~

R/DEploidR.R:152:51: style: Variable or function name should be snake_case.

​                       cex.lab = 1, cex.main = 1, cex.axis = 1){
                                                  ^~~~~~~~

R/DEploidR.R:153:5: style: Variable or function name should be snake_case.

​    rainbowColorBin <- 16
    ^~~~~~~~~~~~~~~

R/DEploidR.R:200:1: style: Variable or function name should be snake_case.

​plotAltVsRef <- function(ref, alt, title = "Alt vs Ref",
^~~~~~~~~~~~

R/DEploidR.R:201:21: style: Variable or function name should be snake_case.

​                    exclude.ref = c(), exclude.alt = c(),
                    ^~~~~~~~~~~

R/DEploidR.R:201:40: style: Variable or function name should be snake_case.

​                    exclude.ref = c(), exclude.alt = c(),
                                       ^~~~~~~~~~~

R/DEploidR.R:202:21: style: Variable or function name should be snake_case.

​                    potentialOutliers = c(), cex.lab = 1, cex.main = 1,
                    ^~~~~~~~~~~~~~~~~

R/DEploidR.R:202:46: style: Variable or function name should be snake_case.

​                    potentialOutliers = c(), cex.lab = 1, cex.main = 1,
                                             ^~~~~~~

R/DEploidR.R:202:59: style: Variable or function name should be snake_case.

​                    potentialOutliers = c(), cex.lab = 1, cex.main = 1,
                                                          ^~~~~~~~

R/DEploidR.R:203:21: style: Variable or function name should be snake_case.

​                    cex.axis = 1){
                    ^~~~~~~~

R/DEploidR.R:207:5: style: Variable or function name should be snake_case.

​    tmpRange <- 1.1 * mean(max(alt), max(ref))
    ^~~~~~~~

R/DEploidR.R:266:1: style: Variable or function name should be snake_case.

​histWSAF <- function(obsWSAF, exclusive = TRUE,
^~~~~~~~

R/DEploidR.R:266:22: style: Variable or function name should be snake_case.

​histWSAF <- function(obsWSAF, exclusive = TRUE,
                     ^~~~~~~

R/DEploidR.R:268:17: style: Variable or function name should be snake_case.

​                cex.lab = 1, cex.main = 1, cex.axis = 1){
                ^~~~~~~

R/DEploidR.R:268:30: style: Variable or function name should be snake_case.

​                cex.lab = 1, cex.main = 1, cex.axis = 1){
                             ^~~~~~~~

R/DEploidR.R:268:44: style: Variable or function name should be snake_case.

​                cex.lab = 1, cex.main = 1, cex.axis = 1){
                                           ^~~~~~~~

R/DEploidR.R:269:5: style: Variable or function name should be snake_case.

​    tmpWSAFIndex <- 1:length(obsWSAF)
    ^~~~~~~~~~~~

R/DEploidR.R:271:9: style: Variable or function name should be snake_case.

​        tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
        ^~~~~~~~~~~~

R/DEploidR.R:271:31: style: Do not place spaces around code in parentheses or square brackets.

​        tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
                              ^

R/DEploidR.R:271:33: style: Do not place spaces around code in parentheses or square brackets.

​        tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
                                ^

R/DEploidR.R:323:1: style: Variable or function name should be snake_case.

​plotWSAFvsPLAF <- function(plaf, obsWSAF, expWSAF = c(),
^~~~~~~~~~~~~~

R/DEploidR.R:323:34: style: Variable or function name should be snake_case.

​plotWSAFvsPLAF <- function(plaf, obsWSAF, expWSAF = c(),
                                 ^~~~~~~

R/DEploidR.R:323:43: style: Variable or function name should be snake_case.

​plotWSAFvsPLAF <- function(plaf, obsWSAF, expWSAF = c(),
                                          ^~~~~~~

R/DEploidR.R:324:23: style: Variable or function name should be snake_case.

​                      potentialOutliers = c(), title = "WSAF vs PLAF",
                      ^~~~~~~~~~~~~~~~~

R/DEploidR.R:325:23: style: Variable or function name should be snake_case.

​                      cex.lab = 1, cex.main = 1, cex.axis = 1){
                      ^~~~~~~

R/DEploidR.R:325:36: style: Variable or function name should be snake_case.

​                      cex.lab = 1, cex.main = 1, cex.axis = 1){
                                   ^~~~~~~~

R/DEploidR.R:325:50: style: Variable or function name should be snake_case.

​                      cex.lab = 1, cex.main = 1, cex.axis = 1){
                                                 ^~~~~~~~

R/DEploidR.R:368:1: style: Lines should not be more than 80 characters.

​#' prop = PG0390CoverageV.deconv$Proportions[dim(PG0390CoverageV.deconv$Proportions)[1],]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DEploidR.R:373:1: style: Variable or function name should be snake_case.

​plotObsExpWSAF <- function(obsWSAF, expWSAF,
^~~~~~~~~~~~~~

R/DEploidR.R:373:28: style: Variable or function name should be snake_case.

​plotObsExpWSAF <- function(obsWSAF, expWSAF,
                           ^~~~~~~

R/DEploidR.R:373:37: style: Variable or function name should be snake_case.

​plotObsExpWSAF <- function(obsWSAF, expWSAF,
                                    ^~~~~~~

R/DEploidR.R:375:23: style: Variable or function name should be snake_case.

​                      cex.lab = 1, cex.main = 1, cex.axis = 1){
                      ^~~~~~~

R/DEploidR.R:375:36: style: Variable or function name should be snake_case.

​                      cex.lab = 1, cex.main = 1, cex.axis = 1){
                                   ^~~~~~~~

R/DEploidR.R:375:50: style: Variable or function name should be snake_case.

​                      cex.lab = 1, cex.main = 1, cex.axis = 1){
                                                 ^~~~~~~~

R/DEploidR.R:411:1: style: Variable or function name should be snake_case.

​computeObsWSAF <- function(alt, ref){
^~~~~~~~~~~~~~

R/DEploidR.R:432:1: style: Variable or function name should be snake_case.

​haplotypePainter <- function(posteriorProbabilities, title = "", labelScaling,
^~~~~~~~~~~~~~~~

R/DEploidR.R:432:30: style: Variable or function name should be snake_case.

​haplotypePainter <- function(posteriorProbabilities, title = "", labelScaling,
                             ^~~~~~~~~~~~~~~~~~~~~~

R/DEploidR.R:432:66: style: Variable or function name should be snake_case.

​haplotypePainter <- function(posteriorProbabilities, title = "", labelScaling,
                                                                 ^~~~~~~~~~~~

R/DEploidR.R:433:25: style: Variable or function name should be snake_case.

​                        numberOfInbreeding = 0){
                        ^~~~~~~~~~~~~~~~~~

R/DEploidR.R:434:5: style: Variable or function name should be snake_case.

​    rainbowColorBin <- 16
    ^~~~~~~~~~~~~~~

R/DEploidR.R:435:5: style: Variable or function name should be snake_case.

​    rainbowColors <- rainbow(rainbowColorBin)
    ^~~~~~~~~~~~~

R/DEploidR.R:437:9: style: Variable or function name should be snake_case.

​        panelSize <- dim(posteriorProbabilities)[2] - numberOfInbreeding
        ^~~~~~~~~

R/DEploidR.R:438:9: style: Variable or function name should be snake_case.

​        rainbowColors <- c(rep("#46a8e1", panelSize),
        ^~~~~~~~~~~~~

R/DEploidR.R:446:5: style: Variable or function name should be snake_case.

​    newXaxt <- round(seq(1, dim(posteriorProbabilities)[1], length.out = 6))
    ^~~~~~~

R/DEploidR.R:449:5: style: Variable or function name should be snake_case.

​    newYaxt <- seq(0, 1, length.out = 3)
    ^~~~~~~

tests/testthat/test-DEploid_tools.R:3:1: style: Variable or function name should be snake_case.

​vcfFileName <- system.file("extdata", "PG0390-C.test.vcf.gz",
^~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:5:1: style: Variable or function name should be snake_case.

​plafFileName <- system.file("extdata", "labStrains.test.PLAF.txt",
^~~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:7:1: style: Variable or function name should be snake_case.

​panelFileName <- system.file("extdata", "labStrains.test.panel.txt",
^~~~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:9:1: style: Variable or function name should be snake_case.

​refFileName <- system.file("extdata", "PG0390-C.test.ref", package = "DEploid")
^~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:10:1: style: Variable or function name should be snake_case.

​altFileName <- system.file("extdata", "PG0390-C.test.alt", package = "DEploid")
^~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:12:1: style: Variable or function name should be snake_case.

​PG0390CoverageVcf <- extractCoverageFromVcf(vcfFileName)
^~~~~~~~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:15:1: style: Variable or function name should be snake_case.

​PG0390Deconv <- dEploid(paste("-vcf", vcfFileName, "-plaf", plafFileName,
^~~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:18:1: style: Variable or function name should be snake_case.

​expWSAF <- t(PG0390Deconv$Haps) %*% prop
^~~~~~~

tests/testthat/test-DEploid_tools.R:21:5: style: Variable or function name should be snake_case.

​    PG0390CoverageTxt <- extractCoverageFromTxt(refFileName, altFileName)
    ^~~~~~~~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:44:5: style: Variable or function name should be snake_case.

​    obsWSAF <- computeObsWSAF(PG0390CoverageVcf$altCount,
    ^~~~~~~

tests/testthat/test-dEploid.R:3:1: style: Variable or function name should be snake_case.

​vcfFileName <- system.file("extdata", "PG0390-C.test.vcf.gz",
^~~~~~~~~~~

tests/testthat/test-dEploid.R:5:1: style: Variable or function name should be snake_case.

​plafFileName <- system.file("extdata", "labStrains.test.PLAF.txt",
^~~~~~~~~~~~

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