Update cerebroApp version in standalone app.

source/R-Portable-Mac/library/cerebroApp/DESCRIPTION

@@ -23,14 +23,14 @@ RemoteType: github
 RemoteHost: api.github.com
 RemoteRepo: cerebroApp
 RemoteUsername: romanhaa
-RemoteRef: merge_packages
-RemoteSha: 867dc3d0b5208fa4381b3f61a45d61c853f80f28
+RemoteRef: develop
+RemoteSha: e830e9b7191db75214a3fca838e95b9373ba75ed
 GithubRepo: cerebroApp
 GithubUsername: romanhaa
-GithubRef: merge_packages
-GithubSHA1: 867dc3d0b5208fa4381b3f61a45d61c853f80f28
+GithubRef: develop
+GithubSHA1: e830e9b7191db75214a3fca838e95b9373ba75ed
 NeedsCompilation: no
-Packaged: 2019-09-24 13:42:33 UTC; ieo4169
+Packaged: 2019-10-15 09:37:34 UTC; ieo4169
 Author: Roman Hillje [aut, cre]
 Maintainer: Roman Hillje <roman.hillje@googlemail.com>
-Built: R 3.5.1; ; 2019-09-24 13:42:35 UTC; unix
+Built: R 3.5.1; ; 2019-10-15 09:37:35 UTC; unix

source/R-Portable-Mac/library/cerebroApp/shiny/enriched_pathways/server.R

@@ -55,6 +55,8 @@ output[["enriched_pathways_by_sample_UI"]] <- renderUI({
         )
       } else if ( sample_data()$enriched_pathways$GSVA$by_sample == "no_gene_sets_enriched" ) {
         textOutput("enriched_pathways_by_sample_table_no_gene_sets_enriched")
+      } else if ( sample_data()$enriched_pathways$GSVA$by_sample == "only_one_sample_in_data_set" ) {
+        textOutput("enriched_pathways_by_sample_table_only_one_sample_in_data_set")
       }
     } else {
       textOutput("enriched_pathways_by_sample_table_missing_gsva")
@@ -217,27 +219,27 @@ output[["enriched_pathways_by_sample_table_present"]] <- DT::renderDataTable(ser
   }
 })
 
-# alternative text
+# alternative text messages
 output[["enriched_pathways_by_sample_table_missing"]] <- renderText({
   "Data not available. Possible reason: Data not generated."
 })
 
-# alternative text
 output[["enriched_pathways_by_sample_table_no_markers_found"]] <- renderText({
   "No marker genes identified to perform pathway enrichment analysis with."
 })
 
-# alternative text
 output[["enriched_pathways_by_sample_table_missing_enrichr"]] <- renderText({
   "Data not available. Possible reasons: Only 1 sample in this data set, no marker genes found or data not generated."
 })
 
-# alternative text
 output[["enriched_pathways_by_sample_table_no_gene_sets_enriched"]] <- renderText({
   "No gene sets were found to be enriched (with the selected statistical thresholds) in any sample."
 })
 
-# alternative text
+output[["enriched_pathways_by_sample_table_only_one_sample_in_data_set"]] <- renderText({
+  "The loaded data set consists of a single sample which means GSVA cannot be applied."
+})
+
 output[["enriched_pathways_by_sample_table_missing_gsva"]] <- renderText({
   "Data not available. Possible reason: Data not generated."
 })
@@ -307,6 +309,8 @@ output[["enriched_pathways_by_cluster_UI"]] <- renderUI({
         )
       } else if ( sample_data()$enriched_pathways$GSVA$by_cluster == "no_gene_sets_enriched" ) {
         textOutput("enriched_pathways_by_cluster_table_no_gene_sets_enriched")
+      } else if ( sample_data()$enriched_pathways$GSVA$by_cluster == "only_one_cluster_in_data_set" ) {
+        textOutput("enriched_pathways_by_cluster_table_only_one_cluster_in_data_set")
       }
     } else {
       textOutput("enriched_pathways_by_cluster_table_missing_gsva")
@@ -469,27 +473,27 @@ output[["enriched_pathways_by_cluster_table_present"]] <- DT::renderDataTable(se
   }
 })
 
-# alternative text
+# alternative text messages
 output[["enriched_pathways_by_cluster_table_missing"]] <- renderText({
   "Data not available. Possible reason: Data not generated."
 })
 
-# alternative text
 output[["enriched_pathways_by_cluster_table_no_markers_found"]] <- renderText({
   "No marker genes identified to perform pathway enrichment analysis with."
 })
 
-# alternative text
 output[["enriched_pathways_by_cluster_table_missing_enrichr"]] <- renderText({
   "Data not available. Possible reasons: Only 1 cluster in this data set, no marker genes found or data not generated."
 })
 
-# alternative text
 output[["enriched_pathways_by_cluster_table_no_gene_sets_enriched"]] <- renderText({
-  "No gene sets were found to be enriched (with the selected statistical thresholds) in any cluster."
+  "Either the loaded data set consists of a single cluster (in which case GSVA cannot be applied) or no gene sets were found to be enriched (with the selected statistical thresholds) in any cluster."
+})
+
+output[["enriched_pathways_by_cluster_table_only_one_cluster_in_data_set"]] <- renderText({
+  "The loaded data set consists of a single cluster which means GSVA cannot be applied."
 })
 
-# alternative text
 output[["enriched_pathways_by_cluster_table_missing_gsva"]] <- renderText({
   "Data not available. Possible reason: Data not generated."
 })

source/R-Portable-Mac/library/cerebroApp/shiny/gene_expression/server.R

@@ -148,8 +148,8 @@ gene_expression_plot_data <- reactive({
   plot_order <- input[["expression_projection_plotting_order"]]
   # check which cells to display
   cells_to_display <- which(
-      grepl(sample_data()$cells$sample, pattern = paste0("^", samples_to_display, "$", collapse = "|")) == TRUE &
-      grepl(sample_data()$cells$cluster, pattern = paste0("^", clusters_to_display, "$", collapse = "|")) == TRUE
+      (sample_data()$cells$sample %in% samples_to_display) &
+      (sample_data()$cells$cluster %in% clusters_to_display)
     )
   # randomly remove cells
   if ( percentage_cells_show < 100 ) {

source/R-Portable-Mac/library/cerebroApp/shiny/gene_set_expression/server.R

@@ -169,8 +169,8 @@ geneSetExpression_plot_data <- reactive({
   plot_order <- input[["geneSetExpression_projection_plotting_order"]]
   # check which cells to display
   cells_to_display <- which(
-      grepl(sample_data()$cells$sample, pattern = paste0("^", samples_to_display, "$", collapse = "|")) == TRUE &
-      grepl(sample_data()$cells$cluster, pattern = paste0("^", clusters_to_display, "$", collapse = "|")) == TRUE
+      (sample_data()$cells$sample %in% samples_to_display) &
+      (sample_data()$cells$cluster %in% clusters_to_display)
     )
   # randomly remove cells
   if ( percentage_cells_show < 100 ) {

source/R-Portable-Mac/library/cerebroApp/shiny/overview/server.R

@@ -113,14 +113,8 @@ output[["overview_projection"]] <- plotly::renderPlotly({
   samples_to_display <- input[["overview_samples_to_display"]]
   clusters_to_display <- input[["overview_clusters_to_display"]]
   cells_to_display <- which(
-      grepl(
-        sample_data()$cells$sample,
-        pattern = paste0("^", samples_to_display, "$", collapse="|")
-      ) &
-      grepl(
-        sample_data()$cells$cluster,
-        pattern = paste0("^", clusters_to_display, "$", collapse="|")
-      )
+      (sample_data()$cells$sample %in% samples_to_display) &
+      (sample_data()$cells$cluster %in% clusters_to_display)
     )
 
   # randomly remove cells
@@ -406,15 +400,9 @@ observeEvent(input[["overview_projection_export"]], {
     samples_to_display <- input[["overview_samples_to_display"]]
     clusters_to_display <- input[["overview_clusters_to_display"]]
     cells_to_display <- which(
-      grepl(
-        sample_data()$cells$sample,
-        pattern = paste0("^", samples_to_display, "$", collapse = "|")
-      ) &
-      grepl(
-        sample_data()$cells$cluster,
-        pattern = paste0("^", clusters_to_display, "$", collapse = "|")
+        (sample_data()$cells$sample %in% samples_to_display) &
+        (sample_data()$cells$cluster %in% clusters_to_display)
       )
-    )
     to_plot <- cbind(
       sample_data()$projections[[ projection_to_display ]][ cells_to_display , ],
       sample_data()$cells[ cells_to_display , ]

source/R-Portable-Mac/library/cerebroApp/shiny/trajectory/server.R

@@ -3,15 +3,8 @@
 ##----------------------------------------------------------------------------##
 
 # what needs to be done
-# - check if trajectory data is available
-# - if not, display a message
-# - if yes, merge with rest of meta data (so cells can be colored by whatever)
-#   - maybe just merge with those cells that info is available for? not ideal
-# - plot trajectory with ggplot -> plotly
-# - second plot to show selected meta data over pseudotime
 # - let user show gene expression as well? probably more complicated
 
-
 # UI element: display results or alternative text
 output[["trajectory_UI"]] <- renderUI({
   if ( length(sample_data()$trajectory$monocle2) > 0 ) {
@@ -253,14 +246,8 @@ output[["trajectory_projection"]] <- plotly::renderPlotly({
   samples_to_display <- input[["trajectory_samples_to_display"]]
   clusters_to_display <- input[["trajectory_clusters_to_display"]]
   cells_to_display <- which(
-      grepl(
-        sample_data()$cells$sample,
-        pattern = paste0("^", samples_to_display, "$", collapse="|")
-      ) &
-      grepl(
-        sample_data()$cells$cluster,
-        pattern = paste0("^", clusters_to_display, "$", collapse="|")
-      )
+      (sample_data()$cells$sample %in% samples_to_display) &
+      (sample_data()$cells$cluster %in% clusters_to_display)
     )
 
   # randomly remove cells
@@ -457,15 +444,9 @@ observeEvent(input[["trajectory_projection_export"]], {
     samples_to_display <- input[["trajectory_samples_to_display"]]
     clusters_to_display <- input[["trajectory_clusters_to_display"]]
     cells_to_display <- which(
-      grepl(
-        sample_data()$cells$sample,
-        pattern = paste0("^", samples_to_display, "$", collapse = "|")
-      ) &
-      grepl(
-        sample_data()$cells$cluster,
-        pattern = paste0("^", clusters_to_display, "$", collapse = "|")
+        (sample_data()$cells$sample %in% samples_to_display) &
+        (sample_data()$cells$cluster %in% clusters_to_display)
       )
-    )
     to_plot <- cbind(
         sample_data()$trajectory$monocle2[[ trajectory_to_display ]][[ "meta" ]][ cells_to_display , ],
         sample_data()$cells[ cells_to_display , ]
@@ -587,14 +568,8 @@ output[["trajectory_density_plot"]] <- plotly::renderPlotly({
   samples_to_display <- input[["trajectory_samples_to_display"]]
   clusters_to_display <- input[["trajectory_clusters_to_display"]]
   cells_to_display <- which(
-      grepl(
-        sample_data()$cells$sample,
-        pattern = paste0("^", samples_to_display, "$", collapse="|")
-      ) &
-      grepl(
-        sample_data()$cells$cluster,
-        pattern = paste0("^", clusters_to_display, "$", collapse="|")
-      )
+      (sample_data()$cells$sample %in% samples_to_display) &
+      (sample_data()$cells$cluster %in% clusters_to_display)
     )
 
   # extract cells to plot

source/R-Portable-Mac/library/cerebroApp/shiny/trajectory/ui.R

@@ -2,11 +2,6 @@
 ## Tab: Trajectory.
 ##----------------------------------------------------------------------------##
 
-# elements needed
-# - user interface
-# - plot 1: trajectory
-# - plot 2: meta data over pseudotime
-
 tab_trajectory <- tabItem(
   tabName = "trajectory",
   uiOutput("trajectory_UI")

source/R-Portable-Mac/library/fastmap/DESCRIPTION

@@ -0,0 +1,30 @@
+Package: fastmap
+Title: Fast Implementation of a Key-Value Store
+Version: 1.0.1
+Authors@R: c(
+    person("Winston", "Chang", email = "winston@rstudio.com", role = c("aut", "cre")),
+    person(given = "RStudio", role = c("cph", "fnd")),
+    person(given = "Tessil", role = "cph", comment = "hopscotch_map library")
+    )
+Description: Fast implementation of a key-value store. Environments are commonly
+    used as key-value stores, but every time a new key is used, it is added to
+    R's global symbol table, causing a small amount of memory leakage. This can
+    be problematic in cases where many different keys are used. Fastmap avoids
+    this memory leak issue by implementing the map using data structures in C++.
+License: MIT + file LICENSE
+Encoding: UTF-8
+LazyData: true
+RoxygenNote: 6.1.1
+Suggests: testthat (>= 2.1.1)
+URL: https://r-lib.github.io/fastmap/, https://github.com/r-lib/fastmap
+BugReports: https://github.com/r-lib/fastmap/issues
+NeedsCompilation: yes
+Packaged: 2019-10-07 23:14:48 UTC; winston
+Author: Winston Chang [aut, cre],
+  RStudio [cph, fnd],
+  Tessil [cph] (hopscotch_map library)
+Maintainer: Winston Chang <winston@rstudio.com>
+Repository: CRAN
+Date/Publication: 2019-10-08 05:20:02 UTC
+Built: R 3.5.2; x86_64-apple-darwin15.6.0; 2019-10-09 08:33:16 UTC; unix
+Archs: fastmap.so.dSYM

source/R-Portable-Mac/library/fastmap/INDEX

@@ -0,0 +1,2 @@
+fastmap                 Create a fastmap object
+key_missing             A missing key object

source/R-Portable-Mac/library/fastmap/LICENSE

@@ -0,0 +1,2 @@
+YEAR: 2019
+COPYRIGHT HOLDER: RStudio

source/R-Portable-Mac/library/fastmap/NAMESPACE

@@ -0,0 +1,7 @@
+# Generated by roxygen2: do not edit by hand
+
+S3method(print,key_missing)
+export(fastmap)
+export(is.key_missing)
+export(key_missing)
+useDynLib(fastmap, .registration = TRUE)

source/R-Portable-Mac/library/fastmap/NEWS.md

@@ -0,0 +1,4 @@
+fastmap 1.0.1
+=============
+
+* Fixed [#13](https://github.com/r-lib/fastmap/issues/13): fastmap.cpp now explicitly includes the algorithm hedder, which is needed on some platforms to successfully compile.

source/R-Portable-Mac/library/fastmap/R/fastmap

@@ -0,0 +1,27 @@
+#  File share/R/nspackloader.R
+#  Part of the R package, http://www.R-project.org
+#
+#  Copyright (C) 1995-2012 The R Core Team
+#
+#  This program is free software; you can redistribute it and/or modify
+#  it under the terms of the GNU General Public License as published by
+#  the Free Software Foundation; either version 2 of the License, or
+#  (at your option) any later version.
+#
+#  This program is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#  GNU General Public License for more details.
+#
+#  A copy of the GNU General Public License is available at
+#  http://www.r-project.org/Licenses/
+
+local({
+    info <- loadingNamespaceInfo()
+    pkg <- info$pkgname
+    ns <- .getNamespace(as.name(pkg))
+    if (is.null(ns))
+        stop("cannot find namespace environment for ", pkg, domain = NA);
+    dbbase <- file.path(info$libname, pkg, "R", pkg)
+    lazyLoad(dbbase, ns, filter = function(n) n != ".__NAMESPACE__.")
+})

source/R-Portable-Mac/library/fastmap/help/AnIndex

@@ -0,0 +1,3 @@
+fastmap	fastmap
+is.key_missing	key_missing
+key_missing	key_missing

source/R-Portable-Mac/library/fastmap/html/00Index.html

@@ -0,0 +1,30 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head><title>R: Fast Implementation of a Key-Value Store</title>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<link rel="stylesheet" type="text/css" href="R.css" />
+</head><body>
+<h1> Fast Implementation of a Key-Value Store
+<img class="toplogo" src="../../../doc/html/Rlogo.svg" alt="[R logo]" />
+</h1>
+<hr/>
+<div style="text-align: center;">
+<a href="../../../doc/html/packages.html"><img class="arrow" src="../../../doc/html/left.jpg" alt="[Up]" /></a>
+<a href="../../../doc/html/index.html"><img class="arrow" src="../../../doc/html/up.jpg" alt="[Top]" /></a>
+</div><h2>Documentation for package &lsquo;fastmap&rsquo; version 1.0.1</h2>
+
+<ul><li><a href="../DESCRIPTION">DESCRIPTION file</a>.</li>
+</ul>
+
+<h2>Help Pages</h2>
+
+
+<table width="100%">
+<tr><td style="width: 25%;"><a href="fastmap.html">fastmap</a></td>
+<td>Create a fastmap object</td></tr>
+<tr><td style="width: 25%;"><a href="key_missing.html">is.key_missing</a></td>
+<td>A missing key object</td></tr>
+<tr><td style="width: 25%;"><a href="key_missing.html">key_missing</a></td>
+<td>A missing key object</td></tr>
+</table>
+</body></html>