set root.dir

cmf1997 · Aug 13, 2024 · 3813ec8 · 3813ec8
1 parent 36fbd5a
commit 3813ec8
Showing 1 changed file with 8 additions and 7 deletions.
diff --git a/vignettes/pbmc_vignette.Rmd b/vignettes/pbmc_vignette.Rmd
@@ -6,6 +6,7 @@ date: 'Compiled: `r format(Sys.Date(), "%B %d, %Y")`'
 
 ```{r init, include=FALSE}
 knitr::opts_chunk$set(echo = TRUE)
+knitr::opts_knit$set(root.dir = "../vignette_data/pbmc_vignette")
 ```
 
 ```{r, include=FALSE}
@@ -71,17 +72,17 @@ metadata generated by `cellranger-atac`, and store the path to the fragment
 file on disk in the Seurat object:
 
 ```{r warning=FALSE, message=FALSE}
-counts <- Read10X_h5(filename = "../vignette_data/10k_pbmc_ATACv2_nextgem_Chromium_Controller_filtered_peak_bc_matrix.h5")
+counts <- Read10X_h5(filename = "10k_pbmc_ATACv2_nextgem_Chromium_Controller_filtered_peak_bc_matrix.h5")
 metadata <- read.csv(
-  file = "../vignette_data/10k_pbmc_ATACv2_nextgem_Chromium_Controller_singlecell.csv",
+  file = "10k_pbmc_ATACv2_nextgem_Chromium_Controller_singlecell.csv",
   header = TRUE,
   row.names = 1
 )
 
 chrom_assay <- CreateChromatinAssay(
   counts = counts,
   sep = c(":", "-"),
-  fragments = '../vignette_data/10k_pbmc_ATACv2_nextgem_Chromium_Controller_fragments.tsv.gz',
+  fragments = "10k_pbmc_ATACv2_nextgem_Chromium_Controller_fragments.tsv.gz",
   min.cells = 10,
   min.features = 200
 )
@@ -119,7 +120,7 @@ Alternatively, you might only have a fragment file. In this case you can create
 a count matrix using the `FeatureMatrix()` function:
 
 ```{r eval=FALSE}
-fragpath <- './vignette_data/10k_pbmc_ATACv2_nextgem_Chromium_Controller_fragments.tsv.gz'
+fragpath <- '10k_pbmc_ATACv2_nextgem_Chromium_Controller_fragments.tsv.gz'
 
 # Define cells
 # If you already have a list of cell barcodes to use you can skip this step
@@ -426,7 +427,7 @@ Alternatively, you can download the pre-processed Seurat object
 
 ```{r warning=FALSE, message=FALSE}
 # Load the pre-processed scRNA-seq data for PBMCs
-pbmc_rna <- readRDS("../vignette_data/pbmc_10k_v3.rds")
+pbmc_rna <- readRDS("pbmc_10k_v3.rds")
 pbmc_rna <- UpdateSeuratObject(pbmc_rna)
 ```
 
@@ -810,7 +811,7 @@ corresponding to the fraction of reads in peaks for each cell.
 
 ```{r eval=FALSE}
 # not run
-total_fragments <- CountFragments('../vignette_data/10k_pbmc_ATACv2_nextgem_Chromium_Controller_fragments.tsv.gz')
+total_fragments <- CountFragments('10k_pbmc_ATACv2_nextgem_Chromium_Controller_fragments.tsv.gz')
 rownames(total_fragments) <- total_fragments$CB
 pbmc$fragments <- total_fragments[colnames(pbmc), "frequency_count"]
 
@@ -844,7 +845,7 @@ pbmc$blacklist_fraction <- FractionCountsInRegion(
 ```
 
 ```{r echo=FALSE, message=FALSE, warning=FALSE}
-saveRDS(object = pbmc, file = "../vignette_data/pbmc.rds")
+saveRDS(object = pbmc, file = "pbmc.rds")
 ```
 
 </details>