adapting the example for the runr functionality to reflect the new lo…

…cation in the inst folder
iSEE · Oct 1, 2024 · 0944a11 · 0944a11
1 parent 9739daa
commit 0944a11
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Showing 3 changed files with 19 additions and 6 deletions.
diff --git a/R/iSEEindex.R b/R/iSEEindex.R
@@ -164,29 +164,38 @@ iSEEindex <- function(bfc, FUN.datasets, FUN.initial = NULL, default.add = TRUE,
 #' ##
 #'
 #' dataset_fun <- function() {
-#'     x <- yaml::read_yaml("tonsil_package.yml")
+#'     x <- yaml::read_yaml(
+#'       system.file("tonsils_example", "tonsil_package.yml", package = "iSEEindex")
+#'     )
 #'     x$datasets
 #' }
 #'
 #' initial_fun <- function() {
-#'     x <- yaml::read_yaml("tonsil_package.yml")
+#'     x <- yaml::read_yaml(
+#'       system.file("tonsils_example", "tonsil_package.yml", package = "iSEEindex")
+#'     )
 #'     x$initial
 #' }
 #'
+#' library("shiny")
 #' header_tonsils <- fluidRow(
 #'   shinydashboard::box(
 #'     width = 12,
 #'     collapsible = TRUE,
 #'     collapsed = TRUE,
 #'     title = "How to explore the Tonsil Atlas datasets",
-#'     includeMarkdown("header_tonsils.md")
+#'     includeMarkdown(
+#'       system.file("tonsils_example", "header_tonsils.md", package = "iSEEindex")
+#'     )
 #'   )
 #' )
 #'
 #' footer_tonsils <- fluidRow(
 #'   shinydashboard::box(
 #'     width = 12,
-#'     includeMarkdown("footer_tonsils.md")
+#'     includeMarkdown(
+#'       system.file("tonsils_example", "footer_tonsils.md", package = "iSEEindex")
+#'     )
 #'   )
 #' )
 #'

diff --git a/inst/tonsils_example/hca_tonsil_epithelial_v2.R b/inst/tonsils_example/hca_tonsil_epithelial_v2.R
@@ -348,7 +348,10 @@ initial[["ComplexHeatmapPlot4"]] <- new("ComplexHeatmapPlot", Assay = "logcounts
 
 ## Adding a tour to tell things to people - they like to hear or read about the data!
 
-tour <- read.delim("tour_tda_epithelial.txt", sep = ";", header = TRUE)
+tour <- read.delim(
+  system.file("tonsils_example/tour_tda_epithelial.txt", package = "iSEEindex"),
+  sep = ";", header = TRUE
+)
 
 
 

diff --git a/inst/tonsils_example/tonsil_package.yml b/inst/tonsils_example/tonsil_package.yml
@@ -53,7 +53,8 @@ initial:
     datasets:
       - Tonsil_epithelial
     title: Tonsil_epithelial configuration 1 (R call)
-    uri: localhost:///Users/fede/Development/iSEEindex/hca_tonsil_epithelial_v2.R
+    uri: rcall://system.file(package='iSEEindex','tonsils_example/hca_tonsil_epithelial_v2.R')
+    # uri: localhost:///Users/fede/Development/iSEEindex/hca_tonsil_epithelial_v2.R
     # uri: rcall://system.file(package='iSEEindex','ReprocessedAllenData_config_01.R')
     description: |
       touring around, first go