Description Usage Arguments Value Examples
Use this function to compute LISI scores of one or more labels.
1 | lisi(X, meta_data, label_colnames, perplexity = 30, nn_eps = 0)
|
X |
A matrix with cells (rows) and features (columns). |
meta_data |
A data frame with one row per cell. |
label_colnames |
Which variables to compute LISI for. |
perplexity |
The effective number of each cell's neighbors. |
nn_eps |
Error bound for nearest neighbor search with |
A data frame of LISI values. Each row is a cell and each column is a different label variable.
1 2 3 4 5 6 | data(sceiad_subset_data)
features <- sceiad_subset_data[, paste0('scviDim_', 1:8)]
metadata <- sceiad_subset_data[,c('Barcode', 'cluster', 'subcluster',
'CellType', 'CellType_predict')]
lisi_scores <- lisi(features, metadata, c('CellType_predict'))
head(lisi_scores)
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