Commit made by the Bioconductor Git-SVN bridge.

Consists of 1 commit(s).

Commit information:

    Commit id: e2e622b
    Commit message:
    Some tweaks to the shinyCOMPASS launcher; plot axis labels for single-facetting case
    Committed by Kevin Ushey <kevinushey at gmail.com>
    Commit date: 2014-03-25T10:33:34-07:00

From: Bioconductor Git-SVN Bridge <[email protected]>

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/COMPASS@87856 bc3139a8-67e5-0310-9ffc-ced21a209358

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: COMPASS
 Type: Package
 Title: Combinatorial Polyfunctionality Analysis of Single Cells
-Version: 1.1.5-1
+Version: 1.1.5-2
 Date: 2014-02-11
 Authors@R: c( person("Lynn", "Lin", role="aut", email="[email protected]"),
     person("Kevin", "Ushey", role=c("aut", "cre"), email="[email protected]"),

R/shinyCOMPASS.R

@@ -13,6 +13,9 @@
 ##' @param facet1,facet2,facet3 Default values for facets in the Shiny app.
 ##'   Each should be the name of a single vector in the metadata.
 ##' @param main A title to give to the heatmap and subset histogram plots.
+##' @param launch Boolean; if \code{TRUE} we launch the Shiny application.
+##'   Otherwise, the user can launch it manually by navigating to the directory
+##'   \code{dir} and running \code{shiny::runApp()}.
 ##' @param ... Optional arguments passed to \code{shiny::runApp}.
 ##' @seealso \code{\link{shinyCOMPASSDeps}}, for identifying packages that you
 ##'   need in order to run the Shiny application.
@@ -26,7 +29,7 @@
 ##'   options(example.ask=TRUE)
 ##' }
 shinyCOMPASS <- function(x, dir=NULL, meta.vars, facet1="None", facet2="None", 
-  facet3="None", main=NA, ...) {
+  facet3="None", main=NA, launch=TRUE, ...) {
 
   if (length(shinyCOMPASSDeps(verbose=FALSE))) {
     message("Error: Can't run the Shiny application as required packages ",
@@ -54,6 +57,8 @@ shinyCOMPASS <- function(x, dir=NULL, meta.vars, facet1="None", facet2="None",
     on.exit(unlink(dir, recursive=TRUE))
   }
 
+  dir <- path.expand(dir)
+
   ## Keep only the metadata variables specified
   iid <- x$data$individual_id
   sid <- x$data$sample_id
@@ -95,7 +100,14 @@ shinyCOMPASS <- function(x, dir=NULL, meta.vars, facet1="None", facet2="None",
   dir.create( file.path(dir, "data"), showWarnings=FALSE )
   saveRDS(x, file=file.path(dir, "data", "data.rds"))
 
-  message("Starting the Shiny application...")
-  runApp(file.path(dir), ...)
+  message("The files necessary for launching the COMPASS Shiny application have ", 
+    "been copied to '", dir, "'.")
+
+  if (launch) {
+    message("Starting the Shiny application...")
+    runApp(file.path(dir), ...)
+  } else {
+    file.path(dir)
+  }
 
 }

inst/shiny/server.R

@@ -365,23 +365,23 @@ shinyServer( function(input, output, session) {
 
       } else if (!is.null(facet1)) {
 
-        p <- ggplot(pf, aes_string(x="factor(1)", y="Score", fill=facet1)) +
+        p <- ggplot(pf, aes_string(y="Score", x=facet1, fill=facet1)) +
           geom_boxplot(outlier.size = 0) +
           geom_point(position=position_jitterdodge()) +
           facet_wrap(~ FunctionalityType, scales="free_y") +
-          xlab("") +
-          theme(
-            axis.text.x=element_blank(),
-            axis.ticks.x=element_blank()
-          )
+          xlab("")
 
       } else {
 
         p <- ggplot(pf, aes_string(x="factor(1)", y="Score")) +
           geom_boxplot(outlier.size = 0) +
-          geom_point(position=position_jitter()) +
+          geom_point(position=position_jitter(width=0.1)) +
           facet_wrap(~ FunctionalityType, scales="free_y") +
-          xlab("")
+          xlab("") +
+          theme(
+            axis.text.x=element_blank(),
+            axis.ticks.x=element_blank()
+          )
 
       }
 

man/shinyCOMPASS.Rd

@@ -4,7 +4,7 @@
 \title{Start a Shiny Application for Visualizing COMPASS Results}
 \usage{
 shinyCOMPASS(x, dir = NULL, meta.vars, facet1 = "None", facet2 = "None",
-  facet3 = "None", main = NA, ...)
+  facet3 = "None", main = NA, launch = TRUE, ...)
 }
 \arguments{
   \item{x}{An object of class \code{COMPASSResult}.}
@@ -25,6 +25,11 @@ shinyCOMPASS(x, dir = NULL, meta.vars, facet1 = "None", facet2 = "None",
   \item{main}{A title to give to the heatmap and subset
   histogram plots.}
 
+  \item{launch}{Boolean; if \code{TRUE} we launch the Shiny
+  application.  Otherwise, the user can launch it manually
+  by navigating to the directory \code{dir} and running
+  \code{shiny::runApp()}.}
+
   \item{...}{Optional arguments passed to
   \code{shiny::runApp}.}
 }