diff --git a/apis/r/.Rbuildignore b/apis/r/.Rbuildignore index bfc33d2bf0..ed2460f60e 100644 --- a/apis/r/.Rbuildignore +++ b/apis/r/.Rbuildignore @@ -25,6 +25,7 @@ tiledbsoma.tar.gz src/libtiledbsoma/build src/libtiledbsoma/test src/libtiledbsoma/docs +src/libtiledbsoma/.editorconfig # vscode ^\.vscode$ diff --git a/apis/r/vignettes/soma-experiment-queries.Rmd b/apis/r/vignettes/soma-experiment-queries.Rmd index 3a4cc6f261..0b4db85131 100644 --- a/apis/r/vignettes/soma-experiment-queries.Rmd +++ b/apis/r/vignettes/soma-experiment-queries.Rmd @@ -24,7 +24,7 @@ library(tiledbsoma) ## Example data -Load the bundled `SOMAExperiment` containing a subsetted version of the 10X genomics [PBMC dataset](https://mojaveazure.github.io/seurat-object/reference/pbmc_small.html) provided by SeuratObject. This will return a `SOMAExperiment` object. +Load the bundled `SOMAExperiment` containing a subsetted version of the 10X genomics [PBMC dataset](https://satijalab.github.io/seurat-object/reference/pbmc_small.html) provided by SeuratObject. This will return a `SOMAExperiment` object. ```{r} experiment <- load_dataset("soma-exp-pbmc-small") @@ -103,7 +103,7 @@ iterator$read_next() iterator$read_complete() ``` -We can also access the expression via `X()`. +We can also access the expression via `X()`. Similarly to `obs()` and `var()`, `X()` is intended for iteration, but in this case we have access to two different iterators, and thus `X()` returns a reader that gives you access to an iterator for `arrow::Table` and one for `Matrix::sparse_matrix`. @@ -168,7 +168,7 @@ As well as the X matrix in two different formats: ```{r} query$X("counts")$tables()$concat() ``` - + `Matrix::sparse_matrix` in `dgTMatrix` format. ```{r} diff --git a/apis/r/vignettes/soma-objects.Rmd b/apis/r/vignettes/soma-objects.Rmd index a42cbff7b1..95ebcb633d 100644 --- a/apis/r/vignettes/soma-objects.Rmd +++ b/apis/r/vignettes/soma-objects.Rmd @@ -22,7 +22,7 @@ library(tiledbsoma) ## Example data -Extract the bundled `SOMAExperiment` containing a subsetted version of the 10X genomics [PBMC dataset](https://mojaveazure.github.io/seurat-object/reference/pbmc_small.html) provided by `SeuratObject`. This will return a file path for the extracted dataset. +Extract the bundled `SOMAExperiment` containing a subsetted version of the 10X genomics [PBMC dataset](https://satijalab.github.io/seurat-object/reference/pbmc_small.html) provided by `SeuratObject`. This will return a file path for the extracted dataset. ```{r} uri <- extract_dataset("soma-exp-pbmc-small") diff --git a/apis/r/vignettes/soma-reading.Rmd b/apis/r/vignettes/soma-reading.Rmd index ca38f20e13..bc16024424 100644 --- a/apis/r/vignettes/soma-reading.Rmd +++ b/apis/r/vignettes/soma-reading.Rmd @@ -19,7 +19,7 @@ library(tiledbsoma) ## Example data -Load the bundled `SOMAExperiment` containing a subsetted version of the 10X genomics [PBMC dataset](https://mojaveazure.github.io/seurat-object/reference/pbmc_small.html) provided by SeuratObject. This will return a `SOMAExperiment` object. This is a small dataset that easily fits into memory, but we'll focus on operations that can easily scale to larger datasets as well. +Load the bundled `SOMAExperiment` containing a subsetted version of the 10X genomics [PBMC dataset](https://satijalab.github.io/seurat-object/reference/pbmc_small.html) provided by SeuratObject. This will return a `SOMAExperiment` object. This is a small dataset that easily fits into memory, but we'll focus on operations that can easily scale to larger datasets as well. ```{r} experiment <- load_dataset("soma-exp-pbmc-small")