Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

make VisiumHD vignettes #33

Open
alikhuseynov opened this issue May 31, 2024 · 0 comments
Open

make VisiumHD vignettes #33

alikhuseynov opened this issue May 31, 2024 · 0 comments
Assignees

Comments

@alikhuseynov
Copy link
Collaborator

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
@alikhuseynov alikhuseynov self-assigned this May 31, 2024
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant