anndata for R has a new home!

Download and load dataset

Let’s use a 10x dataset from the 10x genomics website. You can download it to an anndata object with scanpy as follows:

library(anndata)
library(reticulate)
sc <- import("scanpy")

url <- "https://cf.10xgenomics.com/samples/cell-exp/6.0.0/SC3_v3_NextGem_DI_CellPlex_CSP_DTC_Sorted_30K_Squamous_Cell_Carcinoma/SC3_v3_NextGem_DI_CellPlex_CSP_DTC_Sorted_30K_Squamous_Cell_Carcinoma_count_sample_feature_bc_matrix.h5"
ad <- sc$read_10x_h5("dataset.h5", backup_url = url)

ad

## AnnData object with n_obs × n_vars = 5377 × 36601
##     var: 'gene_ids', 'feature_types', 'genome'

Preprocessing dataset

The resuling dataset is a wrapper for the Python class but behaves very much like an R object:

ad[1:5, 3:5]

## View of AnnData object with n_obs × n_vars = 5 × 3
##     var: 'gene_ids', 'feature_types', 'genome'

dim(ad)

## [1]  5377 36601

You can still call scanpy functions on it, for example to perform preprocessing.

sc$pp$filter_cells(ad, min_genes = 200)
sc$pp$filter_genes(ad, min_cells = 3)
sc$pp$normalize_per_cell(ad)
sc$pp$log1p(ad)

Analysing your dataset in R

You can seamlessly switch back to using your dataset with other R functions. For example, calculating the rowMeans of the expression matrix.

library(Matrix) 
rowMeans(ad$X[1:10,])

## AAACCCAAGCGCGTTC-1 AAACCCAAGGCAATGC-1 AAACCCAGTATCTTCT-1 AAACCCAGTGACAACG-1 
##         0.05451418         0.13627126         0.12637224         0.13958617 
## AAACCCAGTTGAATCC-1 AAACCCATCGGCTTGG-1 AAACGAAAGAGAGCCT-1 AAACGAAAGCTTAAGA-1 
##         0.05979424         0.11365747         0.05011727         0.14347849 
## AAACGAAAGGCACGAT-1 AAACGAAAGGTAGCCA-1 
##         0.12979302         0.12366312

Additional thoughts

¹ When it works. While anndata for R has certainly been useful for us, there is still a lot left to implement. For example, using h5ad-backed AnnData objects does not work yet. If you do encounter an issue, let us know by means of a GitHub Issue. Make sure to include a reproducible example!