docs: allow memory vignette to be built

CCBR · Oct 8, 2024 · 7af5758 · 7af5758
1 parent 1f5adec
commit 7af5758
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Showing 4 changed files with 9 additions and 5 deletions.
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -12,6 +12,5 @@
 ^data-raw$
 ^Dockerfile$
 ^CITATION\.cff$
-^vignettes/memory\.Rmd$
 ^doc$
 ^Meta$
diff --git a/inst/extdata/LIHC_HTseqCounts.txt.gz b/inst/extdata/LIHC_HTseqCounts.txt.gz
diff --git a/inst/extdata/LIHC_PatientData.txt.gz b/inst/extdata/LIHC_PatientData.txt.gz
diff --git a/vignettes/memory.Rmd b/vignettes/memory.Rmd
@@ -23,16 +23,21 @@ library(dplyr)
 library(ggplot2)
 library(glue)
 library(readr)
-# library(reneeTools)
-devtools::load_all()
+library(reneeTools)
 ```
 
 Dataset from: <https://portal.gdc.cancer.gov/projects/TCGA-LIHC>
 
 ```{r data}
-counts <- read_tsv("~/Downloads/LIHC_HTseqCounts.txt") %>%
+counts <- read_tsv(system.file(
+  "extdata", "LIHC_HTseqCounts.txt.gz",
+  package = "reneeTools"
+)) %>%
   rename(gene_id = Gene)
-metadat <- read_tsv("~/Downloads/LIHC_PatientData.txt") %>%
+metadat <- read_tsv(system.file(
+  "extdata", "LIHC_PatientData.txt.gz",
+  package = "reneeTools"
+)) %>%
   select(-sample_id) %>%
   rename(sample_id = barcode)
 renee_ds <- create_reneeDataSet_from_dataframes(metadat, counts) %>%