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.

Sign up for GitHub

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

Update CellChat-vignette.Rmd #175

Open
wants to merge 1 commit into
base: main
Choose a base branch
from
Open

Update CellChat-vignette.Rmd #175

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
4 changes: 2 additions & 2 deletions tutorial/CellChat-vignette.Rmd
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -57,7 +57,7 @@ ptm = Sys.time()
# This is a combined data from two biological conditions: normal and diseases
load("/Users/suoqinjin/Library/CloudStorage/OneDrive-Personal/works/CellChat/tutorial/data_humanSkin_CellChat.rda")
data.input = data_humanSkin$data # normalized data matrix
meta = data_humanSkin$meta # a dataframe with rownames containing cell mata data
meta = data_humanSkin$meta # a dataframe with rownames containing cell meta data
cell.use = rownames(meta)[meta$condition == "LS"] # extract the cell names from disease data

# Subset the input data for CelChat analysis
Expand Down Expand Up @@ -131,7 +131,7 @@ meta <- as.data.frame(SingleCellExperiment::colData(sce)) #
cellChat <- createCellChat(object = sce, group.by = "sce.clusters")
```

If cell mata information is not added when creating CellChat object, USERS can also add it later using `addMeta`, and set the default cell identities using `setIdent`.
If cell meta information is not added when creating CellChat object, USERS can also add it later using `addMeta`, and set the default cell identities using `setIdent`.
```{r eval = FALSE}
cellchat <- addMeta(cellchat, meta = meta)
cellchat <- setIdent(cellchat, ident.use = "labels") # set "labels" as default cell identity
Expand Down