version 0.4.4

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: DEploid
 Type: Package
 Title: Deconvolute Mixed Genomes with Unknown Proportions
-Version: 0.4.3
+Version: 0.4.4
 Authors@R: c(
     person("Joe", "Zhu", role=c("aut", "cre", "cph"), email="joe.zhu@well.ox.ac.uk"),
     person('Jacob', 'Almagro-Garcia', role=c('aut', 'cph')),
@@ -35,7 +35,7 @@ LinkingTo: Rcpp
 RoxygenNote: 6.0.1
 Date: 2017-08-09
 NeedsCompilation: yes
-Packaged: 2017-08-09 20:21:48 UTC; joezhu
+Packaged: 2017-09-01 00:24:49 UTC; joezhu
 Author: Joe Zhu [aut, cre, cph],
   Jacob Almagro-Garcia [aut, cph],
   Gil McVean [aut, cph],
@@ -46,4 +46,4 @@ Author: Joe Zhu [aut, cre, cph],
   Lutz Kettner [com, cph]
 Maintainer: Joe Zhu <joe.zhu@well.ox.ac.uk>
 Repository: CRAN
-Date/Publication: 2017-08-09 20:57:59 UTC
+Date/Publication: 2017-09-01 03:09:29 UTC

MD5

@@ -1,15 +1,15 @@
-fe25858d173d799b7791b1fbe643d5f7 *DESCRIPTION
-d7f3808fb8f81f4820023f8f3ff6d73f *NAMESPACE
+ab020c6fd247593f19934b13a0f9e82d *DESCRIPTION
+60325fac7a82f3e45ef81515447c8dc1 *NAMESPACE
 3f730ab29544fc1d63946a50242f3a42 *R/DEploidR.R
 7efdf7afe8931c93c9c3cdf32a85fb6b *R/RcppExports.R
 856a9b3317faac53312a512e049ca0f9 *R/dEploid.R
-d4b1f3fe520bf3f984aa578b928f72a4 *R/dEploidPlotly.R
+5a2e60ac3ffc29399ffaa1a2308ba8ae *R/dEploidPlotly.R
 db8dd67bf1ee95720e0b4deeefe17540 *README.md
 4b8735c3042553d77ef67496617e1a7a *build/vignette.rds
 461e2dc267742100128d50cd74e757e2 *inst/CITATION
 01c90976b229646ca9b46399709688e3 *inst/doc/dEploid-Arguments.R
 2cbf6a6a60e07984981e6a2329578f8e *inst/doc/dEploid-Arguments.Rmd
-7ad5bd544e465ca7736c57e0bde7815d *inst/doc/dEploid-Arguments.html
+a9c2ba5451ed9582be1822d1ef3c9467 *inst/doc/dEploid-Arguments.html
 2cad08193815864d8a26f8ac768ef199 *inst/extdata/PG0390-C.test.alt
 07eccfaeb952de9e0460bcc12d457b22 *inst/extdata/PG0390-C.test.ref
 cdc601c1d8d4eec2bc80512eb8ee6b6b *inst/extdata/PG0390-C.test.vcf.gz
@@ -26,12 +26,12 @@ d5231f506efc96d0257c95faf60f4c1a *man/extractCoverageFromTxt.Rd
 1d929973d73c6742bd223e1ffc07b15c *man/haplotypePainter.Rd
 d27b68362961277a9dae5718e025b2ee *man/histWSAF.Rd
 c15c6c7d70701d6d454e46553ec8f3fb *man/plotAltVsRef.Rd
-1bfe1926e788ab81b303eb1ab89f25bf *man/plotAltVsRefPlotly.Rd
+4a719f9ddd20b1604d7ac33f64c9c251 *man/plotAltVsRefPlotly.Rd
 2e3ce3260c47e734c3d0aa28cd153abf *man/plotHistWSAFPlotly.Rd
 aa2e2c6ae4087fd61777c9fa17742152 *man/plotObsExpWSAF.Rd
 ab1b443b0af8bf81d85e063f3556e80f *man/plotObsExpWSAFPlotly.Rd
 8f91e514e27c39a978351e2a9976ddc6 *man/plotProportions.Rd
-bcffcc1d30293e4abb6fcc1ef3c39d08 *man/plotWSAFVsPLAFPlotly.Rd
+499310d8b94430a9ff1172326bf9f3d5 *man/plotWSAFVsPLAFPlotly.Rd
 57351dea18413509031f78bd2b106dae *man/plotWSAFvsPLAF.Rd
 c3adb6d6823db1b19840143fa58ba349 *src/DEploid/codeCogs/asympt_expn.h
 9c4cc52f7742819084a453fef38e0288 *src/DEploid/codeCogs/errorfn.h
@@ -99,7 +99,7 @@ c5cc16e00e5cd1b8150a274c1fcfd3ad *src/init.c
 d9780788cb9e10ae63d0cfb4ce81703d *src/r_random_generator.h
 eedb9b59a5a966b63e9e82308caf7349 *src/test_exports.cpp
 e095660d571c0f3ef91ce1211ecb7f76 *tests/testthat.R
-3982e688fb6c251a018d4616267f493a *tests/testthat/test-DEploid_tools.R
+2254c18f55a17646c9bd234fb1e80183 *tests/testthat/test-DEploid_tools.R
 e6096201933e4b6042e165bca5d80db7 *tests/testthat/test-dEploid.R
 f66b335af2d854e56592824fc8df7a0a *tests/testthat/test-r_random-generator.R
 2cbf6a6a60e07984981e6a2329578f8e *vignettes/dEploid-Arguments.Rmd

NAMESPACE

@@ -4,7 +4,7 @@ importFrom("graphics", "abline", "barplot", "hist", "plot", "points", "axis", "l
 importFrom("utils", "read.table")
 importFrom(Rcpp,evalCpp)
 importFrom("magrittr", "%>%")
-importFrom("plotly", "plot_ly", "layout")
+importFrom("plotly", "plot_ly", "layout", "add_trace")
 useDynLib(DEploid, .registration = TRUE)
 export(dEploid)
 export(plotProportions)

R/dEploidPlotly.R

@@ -9,6 +9,8 @@
 #'
 #' @param title Figure title, "Alt vs Ref" by default
 #'
+#' @param potentialOutliers Index of potential outliers.
+#'
 #' @export
 #'
 #' @examples
@@ -23,16 +25,28 @@
 #' PG0390CoverageV = extractCoverageFromVcf(vcfFile)
 #' plotAltVsRefPlotly(PG0390CoverageV$refCount, PG0390CoverageV$altCount)
 #'
-plotAltVsRefPlotly <- function(ref, alt, title = "Alt vs Ref"){
+plotAltVsRefPlotly <- function(ref, alt, title = "Alt vs Ref",
+                               potentialOutliers = c()){
     ratios <- ref / (ref + alt + 0.0000001)
     legendName <- "Ref/(Ref+Alt) Ratio"
-    plot_ly(x = ref, y = alt, type = "scatter", mode = "markers",
+    refvsalt <- data.frame(ref, alt)
+    refvsalt$ref.out <- ifelse(rownames(refvsalt) %in%
+                                  potentialOutliers, ref, NA)
+    refvsalt$alt.out <- ifelse(rownames(refvsalt) %in%
+                                  potentialOutliers, alt, NA)
+    refvsalt$outlier <- ifelse(is.na(refvsalt$ref.out),
+                              "outlier", "normal")
+    plot_ly(data = refvsalt, x = ~ref, y = ~alt,
+            type = "scatter", mode = "markers", name = "normal",
             color = ratios, colors = c("#de2d26", "#2b8cbe"), alpha = 0.8,
-            marker = list(size = 3, line = list(color = "black", width = 0.1),
-                          colorbar = list(title = legendName)
-            ),
+            marker = list(size = 3, colorbar = list(title = legendName)),
+            showlegend = F,
             text = paste("RefCount: ", ref, " ;  ", "AltCount: ", alt)) %>%
-        layout(margin = list(l = 65, r = 25, b = 50, t = 80, pad = 0),
+        add_trace(x = ~ref.out, y = ~alt.out, name = "outlier",
+                  type = "scatter", mode = "markers", symbol = I("x"),
+                  marker = list(size = 4, color = "black"), showlegend = F) %>%
+        layout(autosize = F, width = 650, height = 500,
+               margin = list(l = 65, r = 25, b = 50, t = 80, pad = 0),
                title = title, font = list(size = 18, colot = "black"),
                legend = list(font = list(size = 5)),
                xaxis = list(title = "Reference # Reads", range = c(-5, 200),
@@ -94,7 +108,7 @@ plotHistWSAFPlotly <- function(obsWSAF, exclusive = TRUE,
                                title = "Histogram 0<WSAF<1"){
   tmpWSAFIndex <- 1:length(obsWSAF)
   if (exclusive){
-    tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
+    tmpWSAFIndex <- which(((obsWSAF < 1) * (obsWSAF > 0)) == 1)
   }
   xb <- list(
       start = 0,
@@ -132,6 +146,8 @@ plotHistWSAFPlotly <- function(obsWSAF, exclusive = TRUE,
 #'
 #' @param title Figure title, "WSAF vs PLAF" by default
 #'
+#' @param potentialOutliers Index of potential outliers.
+#'
 #' @export
 #'
 #' @examples
@@ -157,14 +173,26 @@ plotHistWSAFPlotly <- function(obsWSAF, exclusive = TRUE,
 #'                PG0390CoverageV$altCount)
 #'
 plotWSAFVsPLAFPlotly <- function(plaf, obsWSAF, ref, alt,
-                                 title = "WSAF vs PLAF"){
-    plot_ly(x = plaf, y = obsWSAF, type = "scatter", mode = "markers",
-            marker = list(size = 2,
-                          color = "#c64343",
-                          line = list(color = "rgba(152, 0, 0, .8)",
-                                      width = 1)),
+                                 title = "WSAF vs PLAF",
+                                 potentialOutliers = c()){
+    wsafvsplaf <- data.frame(plaf, obsWSAF)
+    wsafvsplaf$plaf.out <- ifelse(rownames(wsafvsplaf) %in%
+                                     potentialOutliers, plaf, NA)
+    wsafvsplaf$obsWSAF.out <- ifelse(rownames(wsafvsplaf) %in%
+                                        potentialOutliers, obsWSAF, NA)
+    wsafvsplaf$outlier <- ifelse(is.na(wsafvsplaf$plaf.out),
+                                "outlier", "normal")
+    plot_ly(data = wsafvsplaf, x = ~plaf, y = ~obsWSAF,
+            type = "scatter", mode = "markers",
+            marker = list(size = 2, color = "#f47142",
+                          line = list(color = "#fc6f3c", width = 1)),
             text = paste("RefCount: ", ref, " ;  ", "AltCount: ", alt)) %>%
-        layout(margin = list(l = 65, r = 25, b = 50, t = 80, pad = 0),
+        add_trace(x = ~plaf.out, y = ~obsWSAF.out, name = "outlier",
+                  type = "scatter", mode = "markers", symbol = I("x"),
+                  marker = list(size = 6, color = "black"),
+                  showlegend = F) %>%
+        layout(autosize = F, width = 500, height = 500,
+               margin = list(l = 65, r = 25, b = 50, t = 80, pad = 0),
                title = title, font = list(size = 18, colot = "black"),
                xaxis = list(title = "PLAF", range = c(0, 1),
                             titlefont = list(size = 18, color = "black"),

inst/doc/dEploid-Arguments.html

@@ -12,7 +12,7 @@
 
 <meta name="author" content="Sha Zhu" />
 
-<meta name="date" content="2017-08-09" />
+<meta name="date" content="2017-09-01" />
 
 <title>Command Line Arguments</title>
 
@@ -70,7 +70,7 @@
 
 <h1 class="title toc-ignore">Command Line Arguments</h1>
 <h4 class="author"><em>Sha Zhu</em></h4>
-<h4 class="date"><em>2017-08-09</em></h4>
+<h4 class="date"><em>2017-09-01</em></h4>
 
 
 

tests/testthat/test-DEploid_tools.R

@@ -43,6 +43,7 @@ test_that("computeObsWSAF", {
 test_that("WSAF Related", {
     obsWSAF <- computeObsWSAF(PG0390CoverageVcf$altCount,
                               PG0390CoverageVcf$refCount)
+    potentialOutliers <- c(5, 12, 25, 30, 35, 50)
     expect_that(histWSAF(obsWSAF), is_a("histogram"))
     png("histWSAF.png")
     histWSAF(obsWSAF)
@@ -52,6 +53,8 @@ test_that("WSAF Related", {
     if (htmlwidgets:::pandoc_available()){
         htmlwidgets::saveWidget(p, file = "histWSAFPlotly.html")
     }
+
+    ####
     expect_null(plotWSAFvsPLAF(plaf, obsWSAF))
     png("WSAFvsPLAF.png")
     plotWSAFvsPLAF(plaf, obsWSAF)
@@ -67,6 +70,29 @@ test_that("WSAF Related", {
     if (htmlwidgets:::pandoc_available()){
         htmlwidgets::saveWidget(p, file = "WSAFvsPLAFPlotly.html")
     }
+
+    ###
+    expect_null(plotWSAFvsPLAF(plaf, obsWSAF,
+                               potentialOutliers = potentialOutliers))
+    png("WSAFvsPLAFOutlier.png")
+    plotWSAFvsPLAF(plaf, obsWSAF, potentialOutliers = potentialOutliers)
+    dev.off()
+    expect_null(plotWSAFvsPLAF(plaf, obsWSAF, expWSAF,
+                               potentialOutliers = potentialOutliers))
+    expect_that(inherits(plotWSAFVsPLAFPlotly(plaf, obsWSAF,
+                                              PG0390CoverageVcf$refCount,
+                                              PG0390CoverageVcf$altCount,
+                                              potentialOutliers =
+                                                  potentialOutliers),
+                         "plotly"), is_true())
+    p <- plotWSAFVsPLAFPlotly(plaf, obsWSAF,
+                              PG0390CoverageVcf$refCount,
+                              PG0390CoverageVcf$altCount,
+                              potentialOutliers = potentialOutliers)
+    if (htmlwidgets:::pandoc_available()){
+        htmlwidgets::saveWidget(p, file = "WSAFvsPLAFPlotlyOutlier.html")
+    }
+    ###
     expect_null(plotObsExpWSAF(obsWSAF, expWSAF))
     png("ObsExpWSAF.png")
     plotObsExpWSAF(obsWSAF, expWSAF)
@@ -97,6 +123,28 @@ test_that("plotAltVsRef", {
 })
 
 
+test_that("plotAltVsRefWithOutliers", {
+    potentialOutliers <- c(1, 10, 20, 30, 40)
+    expect_null(plotAltVsRef(PG0390CoverageVcf$refCount,
+                    PG0390CoverageVcf$altCount,
+                    potentialOutliers = potentialOutliers))
+    png("AltVsRefOutlier.png")
+    plotAltVsRef(PG0390CoverageVcf$refCount, PG0390CoverageVcf$altCount,
+                 potentialOutliers = potentialOutliers )
+    dev.off()
+    expect_that(inherits(plotAltVsRefPlotly(PG0390CoverageVcf$refCount,
+                    PG0390CoverageVcf$altCount,
+                    potentialOutliers = potentialOutliers),
+                         "plotly"), is_true())
+    p <- plotAltVsRefPlotly(PG0390CoverageVcf$refCount,
+                            PG0390CoverageVcf$altCount,
+                            potentialOutliers = potentialOutliers)
+    if (htmlwidgets:::pandoc_available()){
+        htmlwidgets::saveWidget(p, file = "plotAltVsRefPlotlyOutlier.html")
+    }
+})
+
+
 test_that("plotProportion", {
     expect_that(plotProportions(PG0390Deconv$Proportions, ""), is_a("numeric"))
 })