Skip to content

Commit

Permalink
Suggesting very minor edits to Update comp_bio_data_integration.Rmd (#…
Browse files Browse the repository at this point in the history
…694)

Three minor changes, feel free to skip or ignore any or all
- R usually talks about 'packages' rather than 'modules'
- patchwork is imported by Seurat so we can skip library(Seurat)
- the initial Seurat data load step calls it AnnData
  • Loading branch information
eddelbuettel authored Aug 6, 2023
1 parent 8c27415 commit 1226a6f
Showing 1 changed file with 2 additions and 3 deletions.
Original file line number Diff line number Diff line change
Expand Up @@ -40,12 +40,11 @@ This notebook provides a demonstration for integrating two Census datasets using

## Finding and fetching data from mouse liver (10X Genomics and Smart-Seq2)

Let's load all modules needed for this notebook.
Let's load all packages needed for this notebook.

```{r, warning=FALSE, message=FALSE}
library(cellxgene.census)
library(Seurat)
library(patchwork)
```

Now we can open the Census.
Expand All @@ -67,7 +66,7 @@ census_datasets <- as.data.frame(census_datasets$concat())
census_datasets[grep("Liver", census_datasets$dataset_title), ]
```

Now we can use the values from `dataset_id` to query and load an AnnData object with all the cells from those datasets.
Now we can use the values from `dataset_id` to query and load a Seurat object with all the cells from those datasets.

```{r, warning=FALSE, message=FALSE, message=FALSE, results='hide'}
tabula_muris_liver_ids <- c("4546e757-34d0-4d17-be06-538318925fcd", "6202a243-b713-4e12-9ced-c387f8483dea")
Expand Down

0 comments on commit 1226a6f

Please sign in to comment.