knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) knitr::opts_chunk$set(eval = reticulate::py_module_available("anndata"))
The API of anndata for R is very similar to its Python counterpart.
Check out ?anndata
for a full list of the functions provided by this package.
AnnData()
stores a data matrix X
together with annotations
of observations obs
(obsm
, obsp
), variables var
(varm
, varp
),
and unstructured annotations uns
.
Here is an example of how to create an AnnData object with 2 observations 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$X ad$obs ad$obsm[["ones"]] ad$layers[["spliced"]] ad$uns[["b"]]
Read from h5ad format:
read_h5ad("pbmc_1k_protein_v3_processed.h5ad")
You can use any of the regular R indexing methods to subset the AnnData
object.
This will result in a 'View' of the underlying data without needing to store
the same data twice.
view <- ad[, 2] view view$is_view ad[,c("var1", "var2")] ad[-1, ]
The X
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$layers["unspliced"][,c("var2", "var3")]
If you assign an AnnData object to another variable and modify either, both will be modified:
ad2 <- ad ad$X[,2] <- 10 list(ad = ad$X, ad2 = ad2$X)
This is standard Python behaviour but not R. In order to
have two separate copies of an AnnData object, use the $copy()
function:
ad3 <- ad$copy() ad$X[,2] <- c(3, 4) list(ad = ad$X, ad3 = ad3$X)
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