assignCellsByScores | R Documentation |
Assign cell types for each cell based on type scores. Optionally uses 'clusters' to expand annotation.
assignCellsByScores( graph, clf.data, score.info = NULL, clusters = NULL, verbose = 0, uncertainty.thresholds = c(coverage = 0.5, negative = 0.5, positive = 0.75), max.depth = NULL, ... )
graph |
cell graph from Seurat, Pagoda2 or some other tool. Can be either in igraph or adjacency matrix format. Use 'graph=NULL' to skip graph diffusion step and get raw score annotation (useful when debug marker genes). |
clf.data |
classification data from 'getClassificationData' |
score.info |
cell type scores from 'getMarkerScoreInfo' function. Re-estimated if NULL |
clusters |
vector with cluster labels named by cell ids. Used to expand annotation on these clusters. |
verbose |
verbosity level (from 0 to 2) |
max.depth |
maximal depth for which annotation is done. Useful during manual marker selection |
... |
Arguments passed on to |
list with parameters:
annotation: annotation per level
scores: assignment scores per level
annotation.filt: the same as annotation, but cells, which don't pass QC are assigned to NA class
clf_data <- getClassificationData(cm, marker_path) ann_by_level <- assignCellsByScores(graph, clf_data, clusters=clusters)
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