Visualizing the projected query cells on reference via a density plot.

PlotProjection(
  seu.q,
  reference,
  ref.color.by,
  ref.colors = NULL,
  ref.alpha = 0.5,
  ref.size = 0.5,
  ref.emb.col = paste0("UMAP_", 1:2),
  query.reduction = "ref.umap",
  query.size = 1,
  query.alpha = 1,
  split.by = NULL,
  n.row = NULL,
  legend.ncol = 1
)

Arguments

seu.q: A query Seurat object containing the projected reference embeddings.
reference: Reference model.
ref.color.by: Name of column in reference data to be used for coloring points.
ref.colors: Vector of colors to be used for reference data points. Default: NULL
ref.alpha: Alpha value for reference data points. Default: 0.5
ref.size: Size of reference data points. Default: 0.5
ref.emb.col: The column names storing the reference embeddings in reference model.
query.reduction: Reduction name to use for query data. Default: 'ref.umap'
query.size: Size of query data points. Default: 1
query.alpha: Alpha value for query data points. Default: 1
split.by: Column name to split query data by. Default: NULL
n.row: Number of rows for facet_wrap when splitting by column. Default: NULL
legend.ncol: Number of columns for legend. Default: 1

Value

A ggplot object.