From 4d38158ed544340e7e34e642f4dee663bd9068c1 Mon Sep 17 00:00:00 2001 From: Dirk Eddelbuettel Date: Sun, 6 Aug 2023 10:28:13 -0500 Subject: [PATCH] Suggesting very minor edits to Update comp_bio_data_integration.Rmd 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 --- .../vignettes_/comp_bio_data_integration.Rmd | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/api/r/cellxgene.census/vignettes_/comp_bio_data_integration.Rmd b/api/r/cellxgene.census/vignettes_/comp_bio_data_integration.Rmd index 0b4b4c177..6ace48616 100644 --- a/api/r/cellxgene.census/vignettes_/comp_bio_data_integration.Rmd +++ b/api/r/cellxgene.census/vignettes_/comp_bio_data_integration.Rmd @@ -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. @@ -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")