use the existing standard Visium vignettes (both .Rmd and .ipynb) as framework to make new VisiumHD vignettes.
all commits to documentation-devel branch.
Example to load VisiumHD using SFE commit 748f6fd or devel branch
# path to "binned_outputs" directory containing:
└── binned_outputs
├── square_002um
├── square_008um
└── square_016um
dir_hd <- "~/Downloads/Visium_HD_Mouse_Brain/binned_outputs/"
# public dataset -> https://www.10xgenomics.com/datasets/visium-hd-cytassist-gene-expression-libraries-of-mouse-brain-he
sfe_hd <-
read10xVisiumSFE(samples = list.files(dir_hd), # 1:3 resolutions
dirs = dir_hd,
bin_size = c("8", "16"), # this defines which of 1:3 resolutions to load
type = "HDF5", # Note, "sparse" takes longer to load
data = "filtered", # spots under tissue
images = c("lowres"), # for now low res. image only
add_Graph = FALSE # Note, this can take time for VisiumHD for 2 or 8µm res.
)
sfe_hd
use the existing standard Visium vignettes (both
.Rmdand.ipynb) as framework to make new VisiumHD vignettes. all commits todocumentation-develbranch. Example to load VisiumHD using SFE commit748f6fdordevelbranch