Merge branch 'master' into devel

* master: (30 commits)
  increase visualTest threshold
  pass other r check arg
  pass r check arg
  fix link to dendrogram
  New mrkHClust function to plot a dendrogram of subcellular markers
  unit test for knntl logging and none
  private ThetaRegRes nologging function
  Parametrise logging in knntlOptimisation to reduce object size
  add plot3D fig
  remove using animate
  set visualTest threshold for different hosts
  fix link to coc
  code of conduct
  depend on MangoTheCat/visualTest
  suggest rmarkdown
  rmarkdown pack in travis
  add travis file
  remove unexported fun's rd
  fix testing errors
  fix rd warnings
  ...

From: Laurent <lg390@cam.ac.uk>

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pRoloc@120773 bc3139a8-67e5-0310-9ffc-ced21a209358

.Rbuildignore

@@ -3,3 +3,4 @@ vignettes/figure/
 README.md
 vignettes/pRoloc-tutorial.pdf
 sandbox
+.travis.yml

.travis.yml

@@ -0,0 +1,35 @@
+language: r
+r: bioc-devel
+cache: packages
+sudo: true
+
+before_install:
+  - tlmgr install bera nowidow parnotes marginfix etoolbox titlesec sectsty framed enumitem parskip soul placeins footmisc changepage xstring caption mathtools 
+
+apt_packages:
+  - libnetcdf-dev
+  - texlive-full  
+
+r_packages:
+  - covr
+
+r_github_packages:
+  - MangoTheCat/visualTest
+
+r_check_args:
+  --no-vignettes
+  --no-build-vignettes
+
+after_success:
+  - Rscript -e 'covr::codecov()'
+
+# print timings (of examples) and sysinfo
+after_script:
+  - dump_logs_by_extension "timings"
+  - dump_sysinfo
+
+notifications:
+  email:
+    on_success: lg390@cam.ac.uk
+    on_failure: lg390@cam.ac.uk
+

CONDUCT.md

@@ -0,0 +1,30 @@
+# Contributor Code of Conduct
+
+As contributors and maintainers of this project, we pledge to respect
+all people who contribute through reporting issues, posting feature
+requests, updating documentation, submitting pull requests or patches,
+and other activities.
+
+We are committed to making participation in this project a
+harassment-free experience for everyone, regardless of level of
+experience, gender, gender identity and expression, sexual
+orientation, disability, personal appearance, body size, race,
+ethnicity, age, or religion.
+
+Examples of unacceptable behavior by participants include the use of
+sexual language or imagery, derogatory comments or personal attacks,
+trolling, public or private harassment, insults, or other
+unprofessional conduct.
+
+Project maintainers have the right and responsibility to remove, edit,
+or reject comments, commits, code, wiki edits, issues, and other
+contributions that are not aligned to this Code of Conduct. Project
+maintainers who do not follow the Code of Conduct may be removed from
+the project team.
+
+Instances of abusive, harassing, or otherwise unacceptable behavior
+may be reported by opening an issue or contacting one or more of the
+project maintainers.
+
+This Code of Conduct is adapted from the Contributor Covenant, version
+1.0.0, available from http://contributor-covenant.org/version/1/0/0/

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: pRoloc
 Type: Package
 Title: A unifying bioinformatics framework for spatial proteomics
-Version: 1.13.12
+Version: 1.13.13
 Authors@R: c(person(given = "Laurent", family = "Gatto",
 	            email = "lg390@cam.ac.uk", 
                     role = c("aut","cre")),
@@ -38,7 +38,8 @@ Imports:
     proxy,
     FNN,
     BiocGenerics,
-    stats,
+    stats,    
+    dendextend,
     RColorBrewer,
     scales,
     MASS,
@@ -53,12 +54,15 @@ Imports:
     graphics
 Suggests:
     testthat,
+    rmarkdown,
+    visualTest,
     pRolocdata (>= 1.9.4),
     roxygen2,
     synapter,
     xtable,
     tsne,
     hexbin,
+    rgl,
     BiocStyle,
     hpar,
     dplyr,
@@ -99,6 +103,8 @@ Collate:
     phenodisco.R
     plotting.R
     plotting2.R
+    plotting3.R
+    hclust.R
     environment.R
     utils.R
     lopims.R

NAMESPACE

@@ -13,11 +13,14 @@ importFrom("graphics", "abline", "axis", "grid", "legend", "matlines",
            "text", "par", "mtext", "barplot")
 importFrom("stats", "as.formula", "cmdscale", "cov", "dist", "kmeans",
            "mahalanobis", "median", "prcomp", "qchisq", "quantile",
-           "update", "var", "rmultinom", "na.omit")
+           "update", "var", "rmultinom", "na.omit", "hclust",
+           "as.dendrogram")
 importFrom("utils", "combn", "head", "menu", "packageDescription",
            "packageVersion", "read.csv", "setTxtProgressBar",
            "txtProgressBar")
 
+importFrom("dendextend", "set")
+
 importMethodsFrom(MLInterfaces, MLearn,
                   predScore, predScores,
                   predictions)
@@ -34,7 +37,7 @@ importFrom(biomaRt, getBM,
            listAttributes)
 
 importFrom(ggplot2, ggplot, geom_point, theme, scale_size_continuous,
-           xlab, ylab, scale_y_discrete, geom_text,
+           xlab, ylab, scale_y_discrete, geom_text, aes,
            scale_color_manual, element_text, scale_x_discrete)
 
 ## Importing to avoid 'no visible global function definition for' NOTES
@@ -81,6 +84,7 @@ exportMethods(chi2,
               f1Count,
               levelPlot,
               plot,
+              plot3D,
               ## clustering
               ## kmeansClustering,
               ## kmeansOptimisation, kmeansOptimization,
@@ -116,7 +120,9 @@ export(## MSnSet manipulation
     move2Ds,
     addLegend,
     plotDist,
+    mrkHClust,
     highlightOnPlot,
+    highlightOnPlot3D,
     SpatProtVis,
     orgQuants,
     ## -- data checks

NEWS

@@ -1,3 +1,12 @@
+CHANGES IN VERSION 1.13.13
+--------------------------
+ o Added plot3D, equivalent to plot2D, but using rgl in 3 dimensions
+   <2016-09-03 Sat>
+ o Parametrise logging in knntlOptimisation to reduce object size
+   <2016-09-06 Tue>
+ o New mrkHClust function to plot a dendrogram of subcellular markers
+   <2016-09-06 Tue>
+
 CHANGES IN VERSION 1.13.12
 --------------------------
  o Remove verbose argument from getMarkerClasses function

R/hclust.R

@@ -0,0 +1,54 @@
+##' This functions calculates an average protein profile for each
+##' marker class (proteins of unknown localisation are ignored) and
+##' then generates a dendrogram representing the relation between
+##' marker classes. The colours used for the dendrogram labels are
+##' taken from the default colours (see \code{\link{getStockcol}}) so
+##' as to match the colours with other spatial proteomics
+##' visualisations such as \code{\link{plot2D}}.
+##'
+##' @title Draw a dendrogram of subcellular clusters
+##' @param object An instance of class \code{MSnSet}.
+##' @param fcol Feature meta-data label (fData column name) defining
+##'     the groups to be differentiated using different
+##'     colours. Default is \code{markers}.
+##' @param distargs A \code{list} of arguments to be passed to the
+##'     \code{\link[stats]{dist}} function.
+##' @param hclustargs A \code{list} of arguments to be passed to the
+##'     \code{\link[stats]{hclust}} function.
+##' @param plot A \code{logical} defining whether the dendrogram
+##'     should be plotted. Default is \code{TRUE}.
+##' @param ... Additional parameters passed when plotting the
+##'     \code{\link[stats]{dendrogram}}.
+##' @return Invisibly returns a matrix of average occupancy profiles
+##'     for all marker classes defined in \code{fcol}.
+##' @author Laurent Gatto
+##' @examples
+##' library("pRolocdata")
+##' data(dunkley2006)
+##' mrkHClust(dunkley2006)
+mrkHClust <- function(object, fcol = "markers",
+                      distargs, hclustargs,
+                      plot = TRUE,
+                      ...) {
+    object <- markerMSnSet(object)
+    mm <- getMarkers(object, fcol = fcol, verbose = FALSE)
+    umm <- levels(factor(mm))
+    fmat <- matrix(NA, nrow = length(umm), ncol = ncol(object))
+    rownames(fmat) <- umm
+    colnames(fmat) <- sampleNames(object)
+    for (m in umm)
+        fmat[m, ] <- colMeans(exprs(object[mm == m, ]), na.rm = TRUE)
+    ## handling additional dist args
+    if (missing(distargs)) distargs <- list(x = fmat)
+    else distargs <- c(list(x = fmat), distargs)
+    d <- do.call(dist, distargs)
+    ## handling additional hclust args
+    if (missing(hclustargs)) hclustargs <- list(d = d)
+    else hclustargs <- c(list(d = d), hclustargs)
+    hc <- do.call(hclust, hclustargs)
+    hc <- as.dendrogram(hc)
+    i <- match(labels(hc), umm)
+    hc <- set(hc, "labels_colors", getStockcol()[i])
+    if (plot) plot(hc, ...)
+    invisible(fmat)
+}

R/machinelearning-framework-theta.R

@@ -324,8 +324,10 @@ combineThetaRegRes <- function(object) {
     .predictions <- do.call(c, lapply(object, function(z) z@predictions))
     .cmMatrices <- do.call(c, lapply(object, function(z) z@cmMatrices))
     .f1Matrices <- do.call(c, lapply(object, function(z) z@f1Matrices))
-    .names <- paste("times", 1:.times, sep="")
-    names(.f1Matrices) <- .names
+    if (length(.f1Matrices) > 0) {
+        .names <- paste("times", 1:.times, sep = "")
+        names(.f1Matrices) <- .names
+    }
     .otherWeights <- do.call(c, lapply(object, function(z) z@otherWeights))
     .ds <- object[[1]]@datasize
     .test.partitions <- vector("list", 2)