Merge branch 'master' into release-3.5

* master: (175 commits)
  Fix comparison plots
  Bioconductor 3.5 release
  bump x.y.z versions to odd y after creation of 3_5 branch
  bump x.y.z versions to even y prior to creation of 3_5 branch
  Update NEWS and DESCRIPTION
  Version 0.99.15
  Remove dropout.present estimation
  Add limits to zeros plots
  Adjust default splat DE fac params
  Add BPPARAM to scDDSimulate
  Add summariseDiff function
  Version 0.99.14
  Add panel function to vignette
  Change var plot scale
  Run checks
  Update panel functions
  Add makeOverallPanel function
  Add makeDiffPanel function
  Add options to comparison plots
  Version 0.99.13
  ...

From: Luke Zappia <lazappi@users.noreply.github.com>

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/splatter@129246 bc3139a8-67e5-0310-9ffc-ced21a209358

DESCRIPTION

 Package: splatter
 Type: Package
 Title: Simple Simulation of Single-cell RNA Sequencing Data
-Version: 1.0.0
-Date: 2017-04-23
+Version: 1.0.1
+Date: 2017-04-28
 Author: Luke Zappia
 Authors@R:
     c(person("Luke", "Zappia", role = c("aut", "cre"),

NEWS.md

+# 1.0.1
+
+* Fix scales in some difference plots
+* Fix colours in difference plots
+* Fix panel legends
+
+# 1.0.0
+
+* Bioconductor 3.5 release
+
 # 0.99.15
 
 * Add summariseDiff function

R/compare.R

@@ -271,6 +271,8 @@ diffSCESets <- function(sces, ref, point.size = 0.1, point.alpha = 0.1,
 
     if (!(ref %in% names(sces))) {
         stop("'ref' must be the name of an SCESet in 'sces'")
+    } else {
+        ref.idx <- which(names(sces) == ref)
     }
 
     if (!is.null(colours)) {
@@ -278,6 +280,7 @@ diffSCESets <- function(sces, ref, point.size = 0.1, point.alpha = 0.1,
                                    len = length(sces) - 1)
     } else {
         colours <- scales::hue_pal()(length(sces))
+        colours <- colours[-ref.idx]
     }
 
     ref.dim <- dim(sces[[ref]])
@@ -400,7 +403,6 @@ diffSCESets <- function(sces, ref, point.size = 0.1, point.alpha = 0.1,
                                 colour = "Dataset")) +
         geom_hline(yintercept = 0, colour = "red") +
         geom_boxplot() +
-        scale_y_continuous(limits = c(0, 100)) +
         scale_colour_manual(values = colours) +
         ylab(paste("Rank difference percentage zeros")) +
         ggtitle("Difference in zeros per gene") +
@@ -411,7 +413,6 @@ diffSCESets <- function(sces, ref, point.size = 0.1, point.alpha = 0.1,
                                 colour = "Dataset")) +
         geom_hline(yintercept = 0, colour = "red") +
         geom_boxplot() +
-        scale_y_continuous(limits = c(0, 100)) +
         scale_colour_manual(values = colours) +
         ylab(paste("Rank difference percentage zeros")) +
         ggtitle("Difference in zeros per cell") +
@@ -559,7 +560,7 @@ makeCompPanel <- function(comp, title = "Comparison",
         plots[[plot]] <- plots[[plot]] + theme(axis.title.x = element_blank())
     }
 
-    plots$leg <- cowplot::get_legend(plots$p1 +
+    plots$leg <- cowplot::get_legend(plots$p3 +
                                          theme(legend.position = "bottom"))
 
     panel <- cowplot::ggdraw() +
@@ -644,7 +645,7 @@ makeDiffPanel <- function(diff, title = "Difference comparison",
         plots[[plot]] <- plots[[plot]] + theme(axis.title.x = element_blank())
     }
 
-    plots$leg <- cowplot::get_legend(plots$p1 +
+    plots$leg <- cowplot::get_legend(plots$p5 +
                                          theme(legend.position = "bottom"))
 
     panel <- cowplot::ggdraw() +
@@ -743,7 +744,7 @@ makeOverallPanel <- function(comp, diff, title = "Overall comparison",
         plots[[plot]] <- plots[[plot]] + theme(axis.title.x = element_blank())
     }
 
-    plots$leg <- cowplot::get_legend(plots$p1 +
+    plots$leg <- cowplot::get_legend(plots$p7 +
                                          theme(legend.position = "bottom"))
 
     panel <- cowplot::ggdraw() +

README.md

@@ -14,15 +14,15 @@ data. Splatter provides a common interface to multiple simulations that have:
 * Functions for simulating counts using those parameters
 
 Splatter is built on top of [`scater`][scater] and stores simulations in
-`SCESet` objects.
+`SCESet` objects. Splatter also has functions for comparing simulations and real
+datasets.
 
 ## Installation.
 
 ### Development version
 
-Splatter has been accepted into the development version of [Bioconductor][bioc]
-and hence requires the development version of R (>=3.4) and the development
-version of Bioconductor (3.5).
+Splatter has been accepted into the latest version of [Bioconductor][bioc]
+and hence requires the latest version of R (>=3.4).
 
 If you have these installed Splatter can be installed from Bioconductor using
 `biocLite`:
@@ -43,13 +43,6 @@ aren't required for core functionality). Building the vignette may sometimes
 fail when run from the command line, if this happens try running the install
 command in RStudio.
 
-### Release version
-
-The last version of Splatter that is compatible with the current version of
-R (3.3) is v0.99.0 which can be downloaded [here][rel33]. There are no
-significant changes to functionality and this version should be fine for most
-users until the next R/Bioconductor release (in approximately April 2017).
-
 ## Getting started
 
 Once installed the best place to get started is the vignette. For most users
@@ -69,4 +62,4 @@ This is a detailed document that introduces the main features of Splatter.
 [contrib]: https://github.com/Bioconductor/Contributions/issues/209
 [bioc]: https://bioconductor.org/packages/devel/bioc/html/splatter.html
 [vignette]: https://bioconductor.org/packages/devel/bioc/vignettes/splatter/inst/doc/splatter.html
-[rel33]: https://github.com/Oshlack/splatter/releases/tag/v0.99.0
+