Skip to content

Commit ae261ae

Browse files
authored
Update README.md
1 parent f587ebd commit ae261ae

File tree

1 file changed

+3
-3
lines changed

1 file changed

+3
-3
lines changed

README.md

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -106,13 +106,13 @@ The model is used to fit per-cell expectations for each gene assuming no correla
106106

107107
### Choosing different metrics
108108

109-
Above we used `latent` as the input option. This assumes that cells are in an N-dimensional space and similarity between cells is evaluated by computing euclidean distances in this space. Either the results of a dimensionality reduction or modeling procedure can be input here, or when working with spatial data, the per-cell coordinates.
109+
Above we used `latent_obsm_key` as the input option. This assumes that cells are in an N-dimensional space and similarity between cells is evaluated by computing euclidean distances in this space. Either the results of a dimensionality reduction or modeling procedure can be input here, or when working with spatial data, the per-cell coordinates.
110110

111-
Alternately, instead of `latent`, you can specify either `tree` or `distances`.
111+
Alternately, instead of `latent_obsm_key`, you can specify either `tree` or `distances_obsp_key`.
112112

113113
`tree` is used for a developmental lineage. In this form, `tree` should be an `ete3.TreeNode` object representing the root of a Tree with each cell as its leaves. This could be constructed programmatically (see ete3's documentation for details) or if your lineage is stored in a Newick file format, you can load it into an ete3.TreeNode object by running `ete3.Tree('my_newick.txt')`. Note: leaf nodes in the tree must have names that match the column labels in the `counts` input (e.g., cell barcodes).
114114

115-
`distances` is used to specify cell-cell distances directly. The value entered should be a Cells x Cells pandas DataFrame.
115+
`distances_obsp_key` is used to specify cell-cell distances directly. The value entered should be a Cells x Cells matrix in `adata.obsp`.
116116

117117

118118
## Compute the KNN graph

0 commit comments

Comments
 (0)