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We install the blosc package to be able to use Blosc as
the decompression codec, since the data we want to load is
Blosc-compressed.
library(pizzarr)
# The path to the root of the AnnData-Zarr store.
root <- "https://data-1.vitessce.io/0.0.33/main/human-lymph-node-10x-visium/human_lymph_node_10x_visium.h5ad.zarr"
# Open the AnnData-Zarr store as an HttpStore.
store <- HttpStore$new(root)
g <- zarr_open_group(store)
obs_attrs <- g$get_item("obs")$get_attrs()$to_list()
index_colname <- obs_attrs[['_index']]
index_arr <- g$get_item(paste0("obs/", index_colname))$get_item("...")$data
umap_arr <- g$get_item("obsm/X_umap")$get_item("...")$data
cluster_arr <- g$get_item("obs/clusters")$get_item("...")$data
print(dim(umap_arr))
# [1] 3861 2
print(dim(index_arr))
# [1] 3861
print(dim(index_arr))
# [1] 3861
plot(x=umap_arr[,1], y=umap_arr[,2], col=cluster_arr)These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.