From a8340a30c8101474719e6aec2d4e67daf2eb0a79 Mon Sep 17 00:00:00 2001
From: Nuno Agostinho <nunodanielagostinho@gmail.com>
Date: Thu, 13 Apr 2017 02:43:06 +0100
Subject: [PATCH] Import missing function and fix error when vignette tries to
 plot transcripts

---
 NAMESPACE                  | 1 +
 R/analysis_diffSplicing.R  | 2 +-
 vignettes/CLI_tutorial.Rmd | 5 ++++-
 3 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index d15b83ce..882d3bfc 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -153,6 +153,7 @@ importFrom(shiny,plotOutput)
 importFrom(shiny,radioButtons)
 importFrom(shiny,reactive)
 importFrom(shiny,removeModal)
+importFrom(shiny,renderPlot)
 importFrom(shiny,renderText)
 importFrom(shiny,renderUI)
 importFrom(shiny,runApp)
diff --git a/R/analysis_diffSplicing.R b/R/analysis_diffSplicing.R
index 91f2ba89..15288258 100644
--- a/R/analysis_diffSplicing.R
+++ b/R/analysis_diffSplicing.R
@@ -422,7 +422,7 @@ diffAnalyses <- function(psi, groups=NULL,
 #' @param output Shiny ouput
 #' @param session Shiny session
 #' 
-#' @importFrom shiny observe observeEvent updateSelectizeInput
+#' @importFrom shiny observe observeEvent updateSelectizeInput renderPlot
 #' @importFrom shinyjs hide show
 #' @return NULL (this function is used to modify the Shiny session's state)
 diffSplicingServer <- function(input, output, session) {
diff --git a/vignettes/CLI_tutorial.Rmd b/vignettes/CLI_tutorial.Rmd
index 9c6b98a2..3b1e5a08 100644
--- a/vignettes/CLI_tutorial.Rmd
+++ b/vignettes/CLI_tutorial.Rmd
@@ -466,7 +466,7 @@ It is also possible to plot transcripts and proteins related to the gene
 associated to a given splicing event. To retrieve and plot transcript
 information from [ENSEMBL][4]:
 
-```{r plot transcripts}
+```{r plot transcripts, eval=FALSE}
 parsed <- parseSplicingEvent(event)
 info <- queryEnsemblByEvent(event, species="human", assembly="hg19")
 plotTranscripts(info, parsed$pos[[1]])
@@ -475,6 +475,9 @@ plotTranscripts(info, parsed$pos[[1]])
 To retrieve and plot protein information from [UniProt][5]:
 
 ```{r plot proteins}
+parsed <- parseSplicingEvent(event)
+info <- queryEnsemblByEvent(event, species="human", assembly="hg19")
+
 # Some of these transcripts have no corresponding protein
 proteins <- info$Transcript$Translation$id
 protein <- proteins[[6]]