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Update CellChat-vignette.Rmd #175

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4 changes: 2 additions & 2 deletions tutorial/CellChat-vignette.Rmd
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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