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The API of anndata for R is very similar to its Python counterpart.Check out?anndata for a full list of the functionsprovided by this package.

WARNING: The outputs ofthis vignette are not rendered on CRAN due to package size limitations.Please check theGettingstarted vignette in the package documentation.

Creating an AnnData object

AnnData() stores a data matrixX togetherwith annotations of observationsobs (obsm,obsp), variablesvar (varm,varp), and unstructured annotationsuns.

Here is an example of how to create an AnnData object with 2observations and 3 variables.

library(anndata)ad<-AnnData(X =matrix(1:6,nrow =2),obs =data.frame(group =c("a","b"),row.names =c("s1","s2")),var =data.frame(type =c(1L,2L,3L),row.names =c("var1","var2","var3")),layers =list(spliced =matrix(4:9,nrow =2),unspliced =matrix(8:13,nrow =2)  ),obsm =list(ones =matrix(rep(1L,10),nrow =2),rand =matrix(rnorm(6),nrow =2),zeros =matrix(rep(0L,10),nrow =2)  ),varm =list(ones =matrix(rep(1L,12),nrow =3),rand =matrix(rnorm(6),nrow =3),zeros =matrix(rep(0L,12),nrow =3)  ),uns =list(a =1,b =data.frame(i =1:3,j =4:6,value =runif(3)),c =list(c.a =3,c.b =4)  ))ad

You can read the information back out using the$notation.

ad$Xad$obsad$obsm[["ones"]]ad$layers[["spliced"]]ad$uns[["b"]]

Reading / writing AnnData objects

Read from h5ad format:

read_h5ad("pbmc_1k_protein_v3_processed.h5ad")

Creating a view

You can use any of the regular R indexing methods to subset theAnnData object. This will result in a ‘View’ of theunderlying data without needing to store the same data twice.

view<- ad[,2]viewview$is_viewad[,c("var1","var2")]ad[-1, ]

AnnData as a matrix

TheX attribute can be used as an R matrix:

ad$X[,c("var1","var2")]ad$X[-1, , drop=FALSE]ad$X[,2]<-10

You can access a different layer matrix as follows:

ad$layers["unspliced"]ad$layers["unspliced"][,c("var2","var3")]

Note on state

If you assign an AnnData object to another variable and modifyeither, both will be modified:

ad2<- adad$X[,2]<-10list(ad = ad$X,ad2 = ad2$X)

This is standard Python behaviour but not R. In order to have twoseparate copies of an AnnData object, use the$copy()function: