Create reference models

Create reference models

CreateReference(
  umap.model,
  gene.sets,
  meta.data,
  bg.genes = NULL,
  gss.method = NULL,
  colors = NULL,
  text.pos = NULL
)

Arguments

umap.model

a list of models returned from FitEnsemblSVM() or FitEnsemblMultiClassif().

gene.sets

a list or data.frame stores gene sets for calculating gene-set scores.

meta.data

a data.frame contains meta data for reference cells, including the reference UMAP embeddings and cell labels.

bg.genes

a vector stores background genes for calculating gene-set score matrix.

gss.method

method for calculating gene-set scores, one of 'AUCell' and 'UCell'.

colors

a named colors vector for visualizing the reference atlas. Deafult: NULL

text.pos

a data.frame contains some annotated text on reference plot.

Value

a reference.model class