Ran tangle.R

lcolladotor · Jul 3, 2023 · 7d3e4c4 · 7d3e4c4
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diff --git a/05_iSEE_intro.R b/05_iSEE_intro.R
@@ -1,4 +1,4 @@
-## --------------------------------------------------------------------
+## ------------------------------------------------------------
 ## Lets build a simple SummarizedExperiment object following information
 ## from the documentation
 library("SummarizedExperiment")
@@ -42,13 +42,13 @@ rse <- SummarizedExperiment(
 rse
 
 
-## ----isee_basic, eval = FALSE----------------------------------------
+## ----isee_basic, eval = FALSE--------------------------------
 ## ## Let's explore the `rse` object interactively
 ## library("iSEE")
 ## iSEE::iSEE(rse)
 
 
-## ----download_sce_layer----------------------------------------------
+## ----download_sce_layer--------------------------------------
 ## Lets get some data using spatialLIBD
 sce_layer <- spatialLIBD::fetch_data("sce_layer")
 sce_layer
@@ -57,6 +57,6 @@ sce_layer
 lobstr::obj_size(sce_layer)
 
 
-## ----explore_sce_layer, eval = FALSE---------------------------------
+## ----explore_sce_layer, eval = FALSE-------------------------
 ## iSEE::iSEE(sce_layer)
 
diff --git a/11_recount3_DEG_exercise.R b/11_recount3_DEG_exercise.R
@@ -1,4 +1,4 @@
-## ----eval = FALSE----------------------------------------------------
+## ----eval = FALSE--------------------------------------------
 ## recount3::create_rse_manual(
 ##     project = "BRAIN",
 ##     project_home = "data_sources/gtex",

diff --git a/17_spatialLIBD_intro.R b/17_spatialLIBD_intro.R
@@ -1,4 +1,4 @@
-## ----"download_10x_data"---------------------------------------------
+## ----"download_10x_data"-------------------------------------
 ## Download and save a local cache of the data provided by 10x Genomics
 bfc <- BiocFileCache::BiocFileCache()
 lymph.url <-
@@ -14,7 +14,7 @@ lymph.url <-
 lymph.data <- sapply(lymph.url, BiocFileCache::bfcrpath, x = bfc)
 
 
-## ----"extract_files"-------------------------------------------------
+## ----"extract_files"-----------------------------------------
 ## Extract the files to a temporary location
 ## (they'll be deleted once you close your R session)
 xx <- sapply(lymph.data, utils::untar, exdir = file.path(tempdir(), "outs"))
@@ -40,7 +40,7 @@ list.files(lymph.dirs)
 ## 1.4G	genes/genes.gtf
 
 
-## ----"use_gencode_gtf"-----------------------------------------------
+## ----"use_gencode_gtf"---------------------------------------
 ## Download the Gencode v32 GTF file and cache it
 gtf_cache <- BiocFileCache::bfcrpath(
     bfc,
@@ -54,7 +54,7 @@ gtf_cache <- BiocFileCache::bfcrpath(
 gtf_cache
 
 
-## ----wrapper_functions-----------------------------------------------
+## ----wrapper_functions---------------------------------------
 ## Import the data as a SpatialExperiment object using wrapper functions
 ## provided by spatialLIBD
 library("spatialLIBD")
@@ -73,7 +73,7 @@ spe_wrapper
 lobstr::obj_size(spe_wrapper)
 
 
-## ----"run_shiny_app_wrapper"-----------------------------------------
+## ----"run_shiny_app_wrapper"---------------------------------
 ## Run our shiny app
 if (interactive()) {
     vars <- colnames(colData(spe_wrapper))